6d0y

X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding Complex

Method: X-RAY DIFFRACTION D_max: 102.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear cap-binding protein subunit 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 24–790	Not recorded	Nuclear cap-binding protein subunit 2 × 1 （P52298） Peroxisome proliferator-activated receptor gamma coactivator 1-beta × 1 （Q86YN6） MG MAGNESIUM ION × 1 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M magnesium chloride, 0.1 M Tris (pH 7.0), 10% [w/v] polyethylene glycol 8000	Resolution 2.68 Å R-free 0.240

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6D0Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H2T Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG Deposited 2002-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 20–652（633 aa） Fragment：MIF4G DOMAIN, RESIDUES 20-653,701-790 Chain C 702–790（89 aa） Fragment：MIF4G DOMAIN, RESIDUES 20-653,701-790	Mutation：YES Mutation：YES	GDP GUANOSINE-5'-DIPHOSPHATE × 1 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.25 TO 1 % PEG 4000, 100 MM MES PH6, 75 TO 100 MM MAGNESIUM FORMATE, pH 6.00	Resolution 2.10 Å R-free 0.269
1H2U Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG Deposited 2002-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–652（633 aa） Fragment：MIF4G DOMAIN, RESIDUES 20-652,701-790 Chain A 702–790（89 aa） Fragment：MIF4G DOMAIN, RESIDUES 20-652,701-790	Mutation：YES Mutation：YES	GDP GUANOSINE-5'-DIPHOSPHATE × 1 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.25 TO 1 % PEG 4000, 100 MM MES PH6, 75 TO 100 MM MAGNESIUM FORMATE, pH 6.00	Resolution 2.40 Å R-free 0.245
1H2U Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG Deposited 2002-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–652（633 aa） Fragment：MIF4G DOMAIN, RESIDUES 20-652,701-790 Chain B 702–790（89 aa） Fragment：MIF4G DOMAIN, RESIDUES 20-652,701-790	Mutation：YES Mutation：YES	GDP GUANOSINE-5'-DIPHOSPHATE × 1 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.25 TO 1 % PEG 4000, 100 MM MES PH6, 75 TO 100 MM MAGNESIUM FORMATE, pH 6.00	Resolution 2.40 Å R-free 0.245
1H2V Structure of the human nuclear cap-binding-complex (CBC) Deposited 2002-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 20–790（771 aa） Fragment：MIF4G DOMAIN, RESIDUES 20-790	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；10 % PEG6000, 100 MM MES PH6, pH 6.00	Resolution 2.00 Å R-free 0.247
1H6K nuclear Cap Binding Complex Deposited 2001-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–670（651 aa） Fragment：MIF4G DOMAIN Chain A 685–790（106 aa） Fragment：MIF4G DOMAIN	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；SEE REFERENCES, pH 7.50	Resolution 2.00 Å R-free 0.234
1H6K nuclear Cap Binding Complex Deposited 2001-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–670（651 aa） Fragment：MIF4G DOMAIN Chain B 685–790（106 aa） Fragment：MIF4G DOMAIN	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；SEE REFERENCES, pH 7.50	Resolution 2.00 Å R-free 0.234
1H6K nuclear Cap Binding Complex Deposited 2001-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 20–670（651 aa） Fragment：MIF4G DOMAIN Chain C 685–790（106 aa） Fragment：MIF4G DOMAIN	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；SEE REFERENCES, pH 7.50	Resolution 2.00 Å R-free 0.234
1N52 Cap Binding Complex Deposited 2002-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–790（790 aa）	Not recorded	MG MAGNESIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 GOL GLYCEROL × 16 GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.25；298 K；PEG 400, magnesium chloride, Tris, Glycine, Ethylene Glycol , pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.11 Å R-free 0.246
1N54 Cap Binding Complex m7GpppG free Deposited 2002-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–790（790 aa）	Not recorded	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.25；298 K；Peg 400, Magnesium chloride, glycerol, Tris, glycine, ethylene glycol, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.72 Å R-free 0.282
3FEX Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–790（790 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM KCl, 12% PEG 8000, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.55 Å R-free 0.292
3FEX Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–790（790 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM KCl, 12% PEG 8000, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.55 Å R-free 0.292
3FEY Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–790（790 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM MES, pH 6.0, and 8% PEG 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.238
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OOB COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE Deposited 2017-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.	Resolution 2.79 Å R-free 0.229
5OOB COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE Deposited 2017-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.	Resolution 2.79 Å R-free 0.229
5OOB COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE Deposited 2017-08-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.	Resolution 2.79 Å R-free 0.229
5OOB COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE Deposited 2017-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.	Resolution 2.79 Å R-free 0.229
7ABG Human pre-Bact-1 spliceosome Deposited 2020-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric	Chain A5 1–790（790 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å
8BY6 Structure of the human nuclear cap-binding complex bound to NCBP3(560-620) and cap-analogue m7GpppG Deposited 2022-12-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–790（771 aa）	Not recorded	GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å
8PMP Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP Deposited 2023-06-29	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8PNT Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA Deposited 2023-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 20–790（771 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
8SRR Cryo-EM structure of the CBC-ALYREF complex Deposited 2023-05-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–790（790 aa）	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8SUY Cryo-EM structure of the human cap binding complex (CBC) Deposited 2023-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–790（790 aa）	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
9HFL Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA Deposited 2024-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain C 1–790（790 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å

17 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCBP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 2–768； UniProt 24–790

Nuclear cap-binding protein subunit 2

Homo sapiens

UniProt P52298

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–156	Not recorded	Nuclear cap-binding protein subunit 1 × 1 （Q09161） Peroxisome proliferator-activated receptor gamma coactivator 1-beta × 1 （Q86YN6） MG MAGNESIUM ION × 1 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M magnesium chloride, 0.1 M Tris (pH 7.0), 10% [w/v] polyethylene glycol 8000	Resolution 2.68 Å R-free 0.240

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D0Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H2T Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG Deposited 2002-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 1–156（156 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.25 TO 1 % PEG 4000, 100 MM MES PH6, 75 TO 100 MM MAGNESIUM FORMATE, pH 6.00	Resolution 2.10 Å R-free 0.269
1H2U Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG Deposited 2002-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 1–156（156 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.25 TO 1 % PEG 4000, 100 MM MES PH6, 75 TO 100 MM MAGNESIUM FORMATE, pH 6.00	Resolution 2.40 Å R-free 0.245
1H2U Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG Deposited 2002-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 1–156（156 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.25 TO 1 % PEG 4000, 100 MM MES PH6, 75 TO 100 MM MAGNESIUM FORMATE, pH 6.00	Resolution 2.40 Å R-free 0.245
1H2V Structure of the human nuclear cap-binding-complex (CBC) Deposited 2002-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 1–156（156 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；10 % PEG6000, 100 MM MES PH6, pH 6.00	Resolution 2.00 Å R-free 0.247
1H6K nuclear Cap Binding Complex Deposited 2001-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 22–77（56 aa） Fragment：RNP DOMAIN Chain X 79–120（42 aa） Fragment：RNP DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；SEE REFERENCES, pH 7.50	Resolution 2.00 Å R-free 0.234
1H6K nuclear Cap Binding Complex Deposited 2001-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 22–77（56 aa） Fragment：RNP DOMAIN Chain Y 79–120（42 aa） Fragment：RNP DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；SEE REFERENCES, pH 7.50	Resolution 2.00 Å R-free 0.234
1H6K nuclear Cap Binding Complex Deposited 2001-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 22–77（56 aa） Fragment：RNP DOMAIN Chain Z 79–120（42 aa） Fragment：RNP DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；SEE REFERENCES, pH 7.50	Resolution 2.00 Å R-free 0.234
1N52 Cap Binding Complex Deposited 2002-11-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–156（156 aa）	Not recorded	MG MAGNESIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 GOL GLYCEROL × 16 GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.25；298 K；PEG 400, magnesium chloride, Tris, Glycine, Ethylene Glycol , pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.11 Å R-free 0.246
1N54 Cap Binding Complex m7GpppG free Deposited 2002-11-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–156（156 aa）	Not recorded	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.25；298 K；Peg 400, Magnesium chloride, glycerol, Tris, glycine, ethylene glycol, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.72 Å R-free 0.282
3FEX Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–156（156 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM KCl, 12% PEG 8000, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.55 Å R-free 0.292
3FEX Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–156（156 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM KCl, 12% PEG 8000, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.55 Å R-free 0.292
3FEY Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–156（156 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM MES, pH 6.0, and 8% PEG 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.238
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Q 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain T 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain W 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	Resolution 2.80 Å R-free 0.268
5OOB COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE Deposited 2017-08-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.	Resolution 2.79 Å R-free 0.229
5OOB COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE Deposited 2017-08-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.	Resolution 2.79 Å R-free 0.229
5OOB COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE Deposited 2017-08-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.	Resolution 2.79 Å R-free 0.229
5OOB COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE Deposited 2017-08-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.	Resolution 2.79 Å R-free 0.229
7ABG Human pre-Bact-1 spliceosome Deposited 2020-09-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric	Chain A1 1–156（156 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å
8BY6 Structure of the human nuclear cap-binding complex bound to NCBP3(560-620) and cap-analogue m7GpppG Deposited 2022-12-12	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–156（156 aa）	Not recorded	GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å
8PMP Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP Deposited 2023-06-29	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8PNT Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA Deposited 2023-07-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–156（156 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
8SRR Cryo-EM structure of the CBC-ALYREF complex Deposited 2023-05-06	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–156（156 aa）	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8SUY Cryo-EM structure of the human cap binding complex (CBC) Deposited 2023-05-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–156（156 aa）	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
9HFL Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA Deposited 2024-11-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain D 1–156（156 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å

17 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCBP2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 21–176； UniProt 1–156

Peroxisome proliferator-activated receptor gamma coactivator 1-beta

OrganismNot specified

UniProt Q86YN6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 955–984	Non-standard monomer：Yes (specific site not provided by mmCIF)	Nuclear cap-binding protein subunit 1 × 1 （Q09161） Nuclear cap-binding protein subunit 2 × 1 （P52298） MG MAGNESIUM ION × 1 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M magnesium chloride, 0.1 M Tris (pH 7.0), 10% [w/v] polyethylene glycol 8000	Resolution 2.68 Å R-free 0.240

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D0Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3SP6 Structural basis for iloprost as a dual PPARalpha/delta agonist Deposited 2011-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 153–163（11 aa）	Not recorded	IL2 (5E)-5-[(3aS,4R,5R,6aS)-5-hydroxy-4-[(1E,3S,4R)-3-hydroxy-4-methyloct-1-en-6-yn-1-yl]hexahydropentalen-2(1H)-ylidene]pentanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；15% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.21 Å R-free 0.239

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRGC2_HUMAN
Isoform	Q86YN6-5
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 2–31； UniProt 955–984

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6d0y
Deposition date deposition_date	2018-04-11
Structure title title	X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding Complex
Keywords keywords	Cap-binding, m7GpppA, transcription, mRNA; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.64 Å
Radius of gyration Rg (electron density) rg_electron	30.60 Å
Forward intensity I(0) i0	170888000.00
Molecular weight molecular_weight	104850.0 kDa
Excluded volume excluded_volume	131460 Å³
Envelope volume envelope_volume	165400 Å³
Hydration-shell volume shell_volume	44083 Å³
Envelope diameter envelope_diameter	107.7 Å
Shell Rg shell_rg	38.54 Å
Envelope Rg envelope_rg	30.47 Å
Shape Rg shape_rg	30.58 Å
Total Rg total_rg	31.33 Å
Total atoms total_atoms	14475
Residues n_residues	901
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	102.8 Å
Rg (real space) rg_real	31.51 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	1.7090e+08
I(0) uncertainty (real space) i0_real_error	2.9550e+06
Rg (reciprocal space) rg_reciprocal	31.57 Å
I(0) (reciprocal space) i0_reciprocal	170900000.0000
Solution quality estimate total_estimate	0.8899
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.1 Å
Skewness Skewness skewness	0.230
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31800000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.948

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Nuclear cap-binding protein subunit 1
Molecular weight formula_weight	91129.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	14749

MANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPVNPTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELEEAKEKLARQHKRRSDDDDRSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQAAENLYFQGHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Nuclear cap-binding protein subunit 2
Molecular weight formula_weight	20047.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GPLHMGGSPEFPGRLEAADPMSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Peroxisome proliferator-activated receptor gamma coactivator 1-beta
Molecular weight formula_weight	3466.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XSEEALPASGKSKYEAMDFDSLLKEAQQSLH

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
Molecular weight formula_weight	787.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	274

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6d0yA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	6d0yC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	6d0yC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	6d0yC03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

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8. Citations (1)

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Unit-cell length a length_a	78.106 Å
Unit-cell length b length_b	111.897 Å
Unit-cell length c length_c	124.795 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.676 Å
Low-resolution limit resolution_low	39.053 Å
R factor r_factor	0.1850
R_work r_work	0.1812
R_free r_free	0.2401

fit	/app/data/saxs_computation/d0/6d0y/6d0y.fit
pddf	/app/data/pr_computation/d0/6d0y/6d0y.pr.out
profile	/app/data/saxs_computation/d0/6d0y/6d0y.dat

X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding Complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear cap-binding protein subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear cap-binding protein subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Peroxisome proliferator-activated receptor gamma coactivator 1-beta

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)