SAXSdb — 6m8q

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–459	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–459	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

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 6M8Q	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 ligand/ion 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 ligand/ion 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
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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 ligand/ion 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 ligand/ion 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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
9NGO CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (FOCUS MAP) Deposited 2025-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–684（684 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9NH5 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (core region) Deposited 2025-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 9 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 A； PDBConstruct 20–478； UniProt 1–459 Author chain B； PDBConstruct 20–478； UniProt 1–459

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	6m8q
Deposition date deposition_date	2018-08-22
Structure title title	Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531
Keywords keywords	;POLYADENYLATION, METALLO-B-LACTAMASE, PRE-MRNA PROCESSING, ARTEMIS, V(D)J RECOMBINATION, DOUBLE-STRAND BREAK REPAIR, HYDROLASE, RNA BINDING PROTEIN, HYDROXYLASE ;; HYDROLASE
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	30.90 Å
Radius of gyration Rg (electron density) rg_electron	30.23 Å
Forward intensity I(0) i0	174085000.00
Molecular weight molecular_weight	104540.0 kDa
Excluded volume excluded_volume	130530 Å³
Envelope volume envelope_volume	159100 Å³
Hydration-shell volume shell_volume	42510 Å³
Envelope diameter envelope_diameter	96.4 Å
Shell Rg shell_rg	38.59 Å
Envelope Rg envelope_rg	30.08 Å
Shape Rg shape_rg	30.24 Å
Total Rg total_rg	30.92 Å
Total atoms total_atoms	7323
Residues n_residues	904
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	97.3 Å
Rg (real space) rg_real	30.78 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	1.7410e+08
I(0) uncertainty (real space) i0_real_error	2.6190e+06
Rg (reciprocal space) rg_reciprocal	30.83 Å
I(0) (reciprocal space) i0_reciprocal	174100000.0000
Solution quality estimate total_estimate	0.9066
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.3 Å
Skewness Skewness skewness	0.190
Kurtosis Kurtosis kurtosis	-0.605
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	82130000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Cleavage and polyadenylation specificity factor subunit 3
Molecular weight formula_weight	54343.1 kDa
EC 编号 ec_number	3.1.27.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7824

GSSHHHHHHSSGLVPRGSHMSAIPAEESDQLLIRPLGAGQEVGRSCIILEFKGRKIMLDCGIHPGLEGMDALPYIDLIDPAEIDLLLISHFHLDHCGALPWFLQKTSFKGRTFMTHATKAIYRWLLSDYVKVSNISADDMLYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHPELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQININNPFVFKHISNLKSMDHFDDIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIMSEPEEITTMSGQKLPLKMSVDYISFSAHTDYQQTSEFIRALKPPHVILVHGEQNEMARLKAALIREYEDNDEVHIEVHNPRNTEAVTLNFR

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 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine
Molecular weight formula_weight	496.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	484

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6m8qa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.10 — beta-CASP RNA-metabolising hydrolases

Domain ID domain_id	d6m8qb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.10 — beta-CASP RNA-metabolising hydrolases

CATH v4.4 (4 domains)

Domain ID domain_id	6m8qA01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	6m8qA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10890 —

Domain ID domain_id	6m8qB01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	6m8qB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10890 —

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8. Citations (1)

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Unit-cell length a length_a	106.222 Å
Unit-cell length b length_b	106.222 Å
Unit-cell length c length_c	206.035 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.490 Å
Low-resolution limit resolution_low	73.950 Å
R factor r_factor	0.1654
R_work r_work	0.1625
R_free r_free	0.2208

fit	/app/data/saxs_computation/m8/6m8q/6m8q.fit
pddf	/app/data/pr_computation/m8/6m8q/6m8q.pr.out
profile	/app/data/saxs_computation/m8/6m8q/6m8q.dat

Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531

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

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