8pnt

Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA

Method: ELECTRON MICROSCOPY D_max: 101.8 Å Quality: REASONABLE

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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 20–790	Not recorded	Nuclear cap-binding protein subunit 2 × 1 （P52298） Phosphorylated adapter RNA export protein × 2 （Q9H814） 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

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 8PNT	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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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	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 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	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 oligomeric state 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	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 method 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 oligomeric state 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	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 oligomeric state 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	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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state 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	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 experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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
6D0Y X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding Complex Deposited 2018-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 24–790（767 aa）	Not recorded	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
7ABG Human pre-Bact-1 spliceosome Deposited 2020-09-07	Different construct Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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
8SRR Cryo-EM structure of the CBC-ALYREF complex Deposited 2023-05-06	Different construct Different oligomeric state Different ligand/ion 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 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 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 A； PDBConstruct 2–772； UniProt 20–790

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–156	Not recorded	Nuclear cap-binding protein subunit 1 × 1 （Q09161） Phosphorylated adapter RNA export protein × 2 （Q9H814） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8PNT	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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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	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 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	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 oligomeric state 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	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 method 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 oligomeric state 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	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 oligomeric state 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	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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state 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	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 experimental method 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 experimental method 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 oligomeric state Different experimental method 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
6D0Y X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding Complex Deposited 2018-04-11	Different oligomeric state 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 1–156（156 aa）	Not recorded	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
7ABG Human pre-Bact-1 spliceosome Deposited 2020-09-07	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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
8SRR Cryo-EM structure of the CBC-ALYREF complex Deposited 2023-05-06	Different oligomeric state Different ligand/ion 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 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 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 B； PDBConstruct 1–156； UniProt 1–156

Phosphorylated adapter RNA export protein

Homo sapiens

UniProt Q9H814

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–394 Chain D； UniProt 1–394	Not recorded	Nuclear cap-binding protein subunit 1 × 1 （Q09161） Nuclear cap-binding protein subunit 2 × 1 （P52298） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8PNT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XC7 Solution Structure of PHAX-RBD in complex with ssRNA Deposited 2010-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 223–323（101 aa） Fragment：RNA_GG_BIND, RESIDUES 223-323	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；297 K；Ionic strength (raw mmCIF value) 50 NMR sample composition 90% WATER/10% D2O	Resolution not provided
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 structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain N 1–394（394 aa） Chain P 1–394（394 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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHAX_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–394； UniProt 1–394 Author chain D； PDBConstruct 1–394； UniProt 1–394

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	8pnt
Deposition date deposition_date	2023-07-01
最后修订 last_revision	2024-01-17
Structure title title	Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA
Keywords keywords	Nuclear cap-binding complex, PHAX, Pol II transcript metabolism, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	31.91 Å
Radius of gyration Rg (electron density) rg_electron	30.80 Å
Forward intensity I(0) i0	181317000.00
Molecular weight molecular_weight	108130.0 kDa
Excluded volume excluded_volume	135660 Å³
Envelope volume envelope_volume	174080 Å³
Hydration-shell volume shell_volume	45815 Å³
Envelope diameter envelope_diameter	108.4 Å
Shell Rg shell_rg	38.93 Å
Envelope Rg envelope_rg	30.82 Å
Shape Rg shape_rg	30.79 Å
Total Rg total_rg	31.53 Å
Total atoms total_atoms	15133
Residues n_residues	927
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	101.8 Å
Rg (real space) rg_real	31.76 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	1.8130e+08
I(0) uncertainty (real space) i0_real_error	2.5310e+06
Rg (reciprocal space) rg_reciprocal	31.82 Å
I(0) (reciprocal space) i0_reciprocal	181300000.0000
Solution quality estimate total_estimate	0.6974
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.7 Å
Skewness Skewness skewness	0.224
Kurtosis Kurtosis kurtosis	-0.348
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	36370000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.989; Smooth: 0.877

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nuclear cap-binding protein subunit 1
Molecular weight formula_weight	89781.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	15133

MKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPANPTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELEEAKEKLARQHKRRSDDDDRSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQA

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Nuclear cap-binding protein subunit 2
Molecular weight formula_weight	18028.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

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	Phosphorylated adapter RNA export protein
Molecular weight formula_weight	44468.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MALEVGDMEDGQLSDSDSDMTVAPSDRPLQLPKVLGGDSAMRAFQNTATACAPVSHYRAVESVDSSEESFSDSDDDSCLWKRKRQKCFNPPPKPEPFQFGQSSQKPPVAGGKKINNIWGAVLQEQNQDAVATELGILGMEGTIDRSRQSETYNYLLAKKLRKESQEHTKDLDKELDEYMHGGKKMGSKEEENGQGHLKRKRPVKDRLGNRPEMNYKGRYEITAEDSQEKVADEISFRLQEPKKDLIARVVRIIGNKKAIELLMETAEVEQNGGLFIMNGSRRRTPGGVFLNLLKNTPSISEEQIKDIFYIENQKEYENKKAARKRRTQVLGKKMKQAIKSLNFQEDDDTSRETFASDTNEALASLDESQEGHAEAKLEAEEAIEVDHSHDLDIF

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 4 Entity 4 non-polymer

Description description	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	539.2 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.46 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	193335

fit	/app/data/saxs_computation/pn/8pnt/8pnt.fit
pddf	/app/data/pr_computation/pn/8pnt/8pnt.pr.out
profile	/app/data/saxs_computation/pn/8pnt/8pnt.dat

Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA

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

Phosphorylated adapter RNA export protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

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

来源 Source

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)