SAXSdb — 9ngo

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

Cleavage and polyadenylation specificity factor subunit 3

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 H； UniProt 1–684	Not recorded	Cleavage and polyadenylation specificity factor subunit 2 × 1 （Q9P2I0） Symplekin × 1 （Q92797）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.01 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 9NGO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2I7T Structure of human CPSF-73 Deposited 2006-08-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–459（459 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100mM MOPS (pH 6.5), 16% PEG 3350, 300mM sodium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.10 Å R-free 0.276
2I7V Structure of Human CPSF-73 Deposited 2006-08-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–459（459 aa）	Not recorded	ZN ZINC ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100mM MOPS (pH 6.5), 300mM sodium sulfate, 16% PEG 3350, 0.5mM Zinc Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.10 Å R-free 0.252
6M8Q Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531 Deposited 2018-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–459（459 aa）	Not recorded	ZN ZINC ION × 2 JBG N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；Reservoir solution: 100 mM Tris HCl pH 7.0; 0.4 M NaH2PO4; 1.466 K2HPO; 0.2 M NaCl 10 mg/mL Protein solution: CPSF3 protein in; 20 mM Hepes pH 7.7; 150 mM NaCl; 5 % glycerol; 1 mM DTT; 0.5 mM NVP-LTM531 Co-crystallization Protocol: 50 nL of protein mixed with 50 nL of reservoir solution. Crystals grew within 1 day with tetragonal bipyramidal habitus and reached a maximum size of 50 micrometers after 3 days. Cryo-protection Protocol: supplemented reservoir solution with 10 and 20% glycerol, respectively, and subsequently added both solution within 5 min. Crystals incubate for another 5 min before harvesting.	Resolution 2.49 Å R-free 0.221
6M8Q Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531 Deposited 2018-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–459（459 aa）	Not recorded	ZN ZINC ION × 2 JBG N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；Reservoir solution: 100 mM Tris HCl pH 7.0; 0.4 M NaH2PO4; 1.466 K2HPO; 0.2 M NaCl 10 mg/mL Protein solution: CPSF3 protein in; 20 mM Hepes pH 7.7; 150 mM NaCl; 5 % glycerol; 1 mM DTT; 0.5 mM NVP-LTM531 Co-crystallization Protocol: 50 nL of protein mixed with 50 nL of reservoir solution. Crystals grew within 1 day with tetragonal bipyramidal habitus and reached a maximum size of 50 micrometers after 3 days. Cryo-protection Protocol: supplemented reservoir solution with 10 and 20% glycerol, respectively, and subsequently added both solution within 5 min. Crystals incubate for another 5 min before harvesting.	Resolution 2.49 Å R-free 0.221
6V4X Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution Deposited 2019-12-02	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain H 1–684（684 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8T1Q Crystal structure of human CPSF73 catalytic segment in complex with compound 1 Deposited 2023-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–459（459 aa）	Not recorded	XYX 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-5-yl]-~{N}-[3-(4-ethanoylphenyl)phenyl]propanamide × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；18-30% (w/v) PEG3350, 200-250 mM ammonium sulfate and 0.1 M Bis-Tris pH 6.3-6.7	Resolution 1.70 Å R-free 0.215
8T1R Crystal structure of human CPSF73 catalytic segment in complex with compound 2 Deposited 2023-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–459（459 aa）	Not recorded	XZC 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-5-yl]-~{N}-[3-(3-methoxyphenyl)phenyl]propanamide × 1 FE FE (III) ION × 2 SO4 SULFATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；18-30% (w/v) PEG3350, 200-250 mM ammonium sulfate and 0.1 M Bis-Tris pH 6.3-6.7	Resolution 2.20 Å R-free 0.250
9NB1 CRYO-EM STRUCTURE OF human U7 SNRNP WITH MUTANT LSM11 that disrupts contacts with CPSF73 Deposited 2025-02-13	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain H 1–684（684 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.85 Å
9NH5 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (core region) Deposited 2025-02-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain H 1–684（684 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
9NH6 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (COMPOSITE MAP) Deposited 2025-02-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain H 1–684（684 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CPSF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–684； UniProt 1–684

Cleavage and polyadenylation specificity factor subunit 2

Homo sapiens

UniProt Q9P2I0

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 I； UniProt 1–782	Not recorded	Cleavage and polyadenylation specificity factor subunit 3 × 1 （Q9UKF6） Symplekin × 1 （Q92797）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.01 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 9NGO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6URG Cryo-EM structure of human CPSF160-WDR33-CPSF30-CPSF100 PIM complex Deposited 2019-10-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–782（782 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6V4X Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution Deposited 2019-12-02	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain I 1–782（782 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9NB1 CRYO-EM STRUCTURE OF human U7 SNRNP WITH MUTANT LSM11 that disrupts contacts with CPSF73 Deposited 2025-02-13	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain I 1–782（782 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.85 Å
9NH5 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (core region) Deposited 2025-02-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain I 1–782（782 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
9NH6 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (COMPOSITE MAP) Deposited 2025-02-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain I 1–782（782 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CPSF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–782； UniProt 1–782

Symplekin

Homo sapiens

UniProt Q92797

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 J； UniProt 30–1101	Not recorded	Cleavage and polyadenylation specificity factor subunit 3 × 1 （Q9UKF6） Cleavage and polyadenylation specificity factor subunit 2 × 1 （Q9P2I0）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.01 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 9NGO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3O2Q Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex Deposited 2010-07-22	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 30–360（331 aa） Fragment：N-terminal domain	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.242
3O2Q Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex Deposited 2010-07-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 30–360（331 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.242
3O2S Crystal structure of the human symplekin-Ssu72 complex Deposited 2010-07-22	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 30–360（331 aa） Fragment：N-terminal domain	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.32M ammonium sulfate, 26% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.266
3O2T Crystal structure of the N-terminal domain of human Symplekin Deposited 2010-07-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–395（366 aa） Fragment：N-terminal domain	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；50mM Bis-Tris, 40mM ammonium sulfate, 40% (v/v) pentaerythritol ethoxylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.40 Å R-free 0.192
3ODR Crystal Structure of the N-terminal Domain of Human Symplekin Deposited 2010-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–395（395 aa） Fragment：N-terminal domain	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；50MM BIS-TRIS, 40MM AMMONIUM SULFATE, 40% (V/V) PENTAERYTHRITOL ETHOXYLATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.229
3ODS Crystal structure of the K185A mutant of the N-terminal domain of human Symplekin Deposited 2010-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–395（395 aa） Fragment：N-terminal domain	Mutation：K185A	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；50MM BIS-TRIS, 40MM AMMONIUM SULFATE, 40% (V/V) PENTAERYTHRITOL ETHOXYLATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.231
4H3H Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA poymerase II CTD peptide phosphorylated at SER-7 Deposited 2012-09-13	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 30–360（331 aa） Fragment：N-terminal domain, UNP residues 30-360	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate,, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.227
4H3H Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA poymerase II CTD peptide phosphorylated at SER-7 Deposited 2012-09-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 30–360（331 aa） Fragment：N-terminal domain, UNP residues 30-360	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate,, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.227
4H3H Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA poymerase II CTD peptide phosphorylated at SER-7 Deposited 2012-09-13	Different construct 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 A 30–360（331 aa） Fragment：N-terminal domain, UNP residues 30-360	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate,, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.227
4H3H Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA poymerase II CTD peptide phosphorylated at SER-7 Deposited 2012-09-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 30–360（331 aa） Fragment：N-terminal domain, UNP residues 30-360	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate,, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.227
4H3K Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA polymerase II CTD peptide phosphorylated at Ser-2, Ser-5 and Ser-7 Deposited 2012-09-13	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 30–360（331 aa） Fragment：N-terminal domain, UNP residues 30-360	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.233
4H3K Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA polymerase II CTD peptide phosphorylated at Ser-2, Ser-5 and Ser-7 Deposited 2012-09-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 30–360（331 aa） Fragment：N-terminal domain, UNP residues 30-360	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.233
4H3K Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA polymerase II CTD peptide phosphorylated at Ser-2, Ser-5 and Ser-7 Deposited 2012-09-13	Different construct 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 A 30–360（331 aa） Fragment：N-terminal domain, UNP residues 30-360	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.233
4H3K Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA polymerase II CTD peptide phosphorylated at Ser-2, Ser-5 and Ser-7 Deposited 2012-09-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 30–360（331 aa） Fragment：N-terminal domain, UNP residues 30-360	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.233
6V4X Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution Deposited 2019-12-02	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain J 30–1101（1072 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9N96 CRYO-EM STRUCTURE OF human U7 SM RING IN COMPLEX WITH SYMPLEKIN N-TERMINAL DOMAIN Deposited 2025-02-10	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: decameric	Chain J 30–1101（1072 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9NB1 CRYO-EM STRUCTURE OF human U7 SNRNP WITH MUTANT LSM11 that disrupts contacts with CPSF73 Deposited 2025-02-13	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain J 30–1101（1072 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.85 Å
9NH5 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (core region) Deposited 2025-02-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain J 30–1101（1072 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
9NH6 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (COMPOSITE MAP) Deposited 2025-02-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain J 30–1101（1072 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å

12 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYMPK_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain J； PDBConstruct 1–1072； UniProt 30–1101

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ngo
Deposition date deposition_date	2025-02-22
Structure title title	CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (FOCUS MAP)
Keywords keywords	;Methylated RNA, 3' end processing, U7 snRNP, Histone pre-mRNA, 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	30.85 Å
Radius of gyration Rg (electron density) rg_electron	30.54 Å
Forward intensity I(0) i0	58407600.00
Molecular weight molecular_weight	61724.0 kDa
Excluded volume excluded_volume	78252 Å³
Envelope volume envelope_volume	107000 Å³
Hydration-shell volume shell_volume	30468 Å³
Envelope diameter envelope_diameter	117.3 Å
Shell Rg shell_rg	35.61 Å
Envelope Rg envelope_rg	30.97 Å
Shape Rg shape_rg	30.53 Å
Total Rg total_rg	31.11 Å
Total atoms total_atoms	4334
Residues n_residues	546
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	111.0 Å
Rg (real space) rg_real	31.00 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	5.8410e+07
I(0) uncertainty (real space) i0_real_error	8.8260e+05
Rg (reciprocal space) rg_reciprocal	30.94 Å
I(0) (reciprocal space) i0_reciprocal	58400000.0000
Solution quality estimate total_estimate	0.8416
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.6 Å
Skewness Skewness skewness	0.483
Kurtosis Kurtosis kurtosis	-0.066
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17570000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.751; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.759; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cleavage and polyadenylation specificity factor subunit 3
Molecular weight formula_weight	77580.9 kDa
EC 编号 ec_number	3.1.27.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	4334

MSAIPAEESDQLLIRPLGAGQEVGRSCIILEFKGRKIMLDCGIHPGLEGMDALPYIDLIDPAEIDLLLISHFHLDHCGALPWFLQKTSFKGRTFMTHATKAIYRWLLSDYVKVSNISADDMLYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHPELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQININNPFVFKHISNLKSMDHFDDIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIMSEPEEITTMSGQKLPLKMSVDYISFSAHTDYQQTSEFIRALKPPHVILVHGEQNEMARLKAALIREYEDNDEVHIEVHNPRNTEAVTLNFRGEKLAKVMGFLADKKPEQGQRVSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFNLLCYQLQKLTGDVEELEIQEKPALKVFKNITVIQEPGMVVLEWLANPSNDMYADTVTTVILEVQSNPKIRKGAVQKVSKKLEMHVYSKRLEIMLQDIFGEDCVSVKDDSILSVTVDGKTANLNLETRTVECEEGSEDDESLREMVELAAQRLYEALTPVH

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	Cleavage and polyadenylation specificity factor subunit 2
Molecular weight formula_weight	88597.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MTSIIKLTTLSGVQEESALCYLLQVDEFRFLLDCGWDEHFSMDIIDSLRKHVHQIDAVLLSHPDPLHLGALPYAVGKLGLNCAIYATIPVYKMGQMFMYDLYQSRHNTEDFTLFTLDDVDAAFDKIQQLKFSQIVNLKGKGHGLSITPLPAGHMIGGTIWKIVKDGEEEIVYAVDFNHKREIHLNGCSLEMLSRPSLLITDSFNATYVQPRRKQRDEQLLTNVLETLRGDGNVLIAVDTAGRVLELAQLLDQIWRTKDAGLGVYSLALLNNVSYNVVEFSKSQVEWMSDKLMRCFEDKRNNPFQFRHLSLCHGLSDLARVPSPKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNPSEKITEIELRKRVKLEGKELEEYLEKEKLKKEAAKKLEQSKEADIDSSDESDIEEDIDQPSAHKTKHDLMMKGEGSRKGSFFKQAKKSYPMFPAPEERIKWDEYGEIIKPEDFLVPELQATEEEKSKLESGLTNGDEPMDQDLSDVPTKCISTTESIEIKARVTYIDYEGRSDGDSIKKIINQMKPRQLIIVHGPPEASQDLAECCRAFGGKDIKVYMPKLHETVDATSETHIYQVRLKDSLVSSLQFCKAKDAELAWIDGVLDMRVSKVDTGVILEEGELKDDGEDSEMQVEAPSDSSVIAQQKAMKSLFGDDEKETGEESEIIPTLEPLPPHEVPGHQSVFMNEPRLSDFKQVLLREGIQAEFVGGVLVCNNQVAVRRTETGRIGLEGCLCQDFYRIRDLLYEQYAIV

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 3 Entity 3 polymer

Description description	Symplekin
Molecular weight formula_weight	120355.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MTTSERVVDLLNQAALITNDSKITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGFIEEACKRDIELLLKLIANLNMLLRDENVNVVKKAILTMTQLYKVALQWMVKSRVISELQEACWDMVSAMAGDIILLLDSDNDGIRTHAIKFVEGLIVTLSPRMADSEIPRRQEHDISLDRIPRDHPYIQYNVLWEEGKAALEQLLKFMVHPAISSINLTTALGSLANIARQRPMFMSEVIQAYETLHANLPPTLAKSQVSSVRKNLKLHLLSVLKHPASLEFQAQITTLLVDLGTPQAEIARNMPSSKDTRKRPRDDSDSTLKKMKLEPNLGEDDEDKDLEPGPSGTSKASAQISGQSDTDITAEFLQPLLTPDNVANLVLISMVYLPEAMPASFQAIYTPVESAGTEAQIKHLARLMATQMTAAGLGPGVEQTKQCKEEPKEEKVVKTESVLIKRRLSAQGQAISVVGSLSSMSPLEEEAPQAKRRPEPIIPVTQPRLAGAGGRKKIFRLSDVLKPLTDAQVEAMKLGAVKRILRAEKAVACSGAAQVRIKILASLVTQFNSGLKAEVLSFILEDVRARLDLAFAWLYQEYNAYLAAGASGSLDKYEDCLIRLLSGLQEKPDQKDGIFTKVVLEAPLITESALEVVRKYCEDESRTYLGMSTLRDLIFKRPSRQFQYLHVLLDLSSHEKDKVRSQALLFIKRMYEKEQLREYVEKFALNYLQLLVHPNPPSVLFGADKDTEVAAPWTEETVKQCLYLYLALLPQNHKLIHELAAVYTEAIADIKRTVLRVIEQPIRGMGMNSPELLLLVENCPKGAETLVTRCLHSLTDKVPPSPELVKRVRDLYHKRLPDVRFLIPVLNGLEKKEVIQALPKLIKLNPIVVKEVFNRLLGTQHGEGNSALSPLNPGELLIALHNIDSVKCDMKSIIKATNLCFAERNVYTSEVLAVVMQQLMEQSPLPMLLMRTVIQSLTMYPRLGGFVMNILSRLIMKQVWKYPKVWEGFIKCCQRTKPQSFQVILQLPPQQLGAVFDKCPELREPLLAHVRSFTPHQQAHIPNSIMTILEAS

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

▶

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	3.01 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	168875

fit	/app/data/saxs_computation/ng/9ngo/9ngo.fit
pddf	/app/data/pr_computation/ng/9ngo/9ngo.pr.out
profile	/app/data/saxs_computation/ng/9ngo/9ngo.dat

CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (FOCUS MAP)

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

Cleavage and polyadenylation specificity factor subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Cleavage and polyadenylation specificity factor subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Symplekin

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 (3)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)