SAXSdb — 4ggc

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

Cell division cycle protein 20 homolog

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 161–477	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM MES, 15% (w/v) PEG 6000, and 5% MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.35 Å R-free 0.146

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 4GGC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GGA Structural Analysis of Human Cdc20 Supports Multi-site Degron Recognition by APC/C Deposited 2012-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 81–499（419 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；100 mM Na citrate, 15 % (w/v) PEG 6000, and 4% MPD, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.04 Å R-free 0.203
4GGD Structural analysis of human Cdc20 supports multisite degron recognition by APC/C. Deposited 2012-08-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 71–499（429 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions sitting-drop vapor diffusion；pH 9.3；293 K；50 mM CAPSO, 5% (w/v) PEG 6000, and 15.5 % MPD, pH 9.3, sitting-drop vapor diffusion, temperature 293K	Resolution 2.44 Å R-free 0.201
4GGD Structural analysis of human Cdc20 supports multisite degron recognition by APC/C. Deposited 2012-08-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 71–499（429 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions sitting-drop vapor diffusion；pH 9.3；293 K；50 mM CAPSO, 5% (w/v) PEG 6000, and 15.5 % MPD, pH 9.3, sitting-drop vapor diffusion, temperature 293K	Resolution 2.44 Å R-free 0.201
4N14 Crystal structure of Cdc20 and apcin complex Deposited 2013-10-03	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 165–477（313 aa） Fragment：WD domain residues 165-477	Not recorded	WR7 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl [(1R)-2,2,2-trichloro-1-(pyrimidin-2-ylamino)ethyl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM MES, 15% (w/v) PEG 6000, and 5% MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.213
5G04 Structure of the human APC-Cdc20-Hsl1 complex Deposited 2016-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain R 1–499（499 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES, 150MM NACL, 0. 5MM TCEP；pH 8；20MM HEPES, 150MM NACL, 0. 5MM TCEP cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 3.90 Å
5KHR Model of human Anaphase-promoting complex/Cyclosome complex (APC15 deletion mutant) in complex with the E2 UBE2C/UBCH10 poised for ubiquitin ligation to substrate (APC/C-CDC20-substrate-UBE2C) Deposited 2016-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain R 1–499（499 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
5KHU Model of human Anaphase-promoting complex/Cyclosome (APC15 deletion mutant), in complex with the Mitotic checkpoint complex (APC/C-CDC20-MCC) based on cryo EM data at 4.8 Angstrom resolution Deposited 2016-06-15	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 × 23 PDB declaration: 23-meric	Chain R 1–499（499 aa） Chain S 1–499（499 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
5LCW Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 4.2 angstrom resolution Deposited 2016-06-22	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 × 23 PDB declaration: 23-meric	Chain Q 126–499（374 aa） Chain R 1–499（499 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6F0X Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20 Deposited 2017-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain Q 1–499（499 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6Q6G Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D1 box class Deposited 2018-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain R 1–499（499 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Hepes, 150mM NaCl, 0.5mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6Q6H Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D2 box class Deposited 2018-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain R 1–499（499 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Hepes, 150mM NaCl, 0.5mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6TLJ Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 3.8 angstrom resolution Deposited 2019-12-02	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 × 23 PDB declaration: 23-meric	Chain Q 126–499（374 aa） Chain R 1–499（499 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9I68 Crystal structure of human Cdc20 bound to synthetic D-box peptide D21 Deposited 2025-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–499（499 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；10 % MPD, 12-14 % PEG 6000, 0.1 M MES pH 6.5	Resolution 1.50 Å R-free 0.194
9I69 Crystal structure of human Cdc20 bound to synthetic D-box peptide D20 Deposited 2025-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–499（499 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；10 % MPD, 12-14 % PEG 6000, 0.1 M MES pH 6.5	Resolution 1.46 Å R-free 0.184
9I6A Crystal structure of human Cdc20 bound to synthetic D-box peptide D7 Deposited 2025-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–499（499 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；10 % MPD, 12-14 % PEG 6000, 0.1 M MES pH 6.5	Resolution 1.92 Å R-free 0.231
9N9R Model of APC/C-CDC20-UBE2C from H2A/H2B-bound complex Deposited 2025-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain R 1–499（499 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
9N9S Model of APC/C-CDC20-UBE2C from H3/H4-bound complex Deposited 2025-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain R 1–499（499 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å

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

View Construct and Data Evidence

UniProt name	CDC20_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–318； UniProt 161–477

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	4ggc
Deposition date deposition_date	2012-08-06
Structure title title	Structural Analysis of Human Cdc20 Supports Multi-site Degron Recognition by APC/C
Keywords keywords	cell cycle, mitosis, securin, ubiquitination, WD40; CELL CYCLE
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	19.48 Å
Radius of gyration Rg (electron density) rg_electron	18.40 Å
Forward intensity I(0) i0	21535100.00
Molecular weight molecular_weight	34811.0 kDa
Excluded volume excluded_volume	43245 Å³
Envelope volume envelope_volume	48396 Å³
Hydration-shell volume shell_volume	21255 Å³
Envelope diameter envelope_diameter	61.1 Å
Shell Rg shell_rg	25.41 Å
Envelope Rg envelope_rg	18.62 Å
Shape Rg shape_rg	18.38 Å
Total Rg total_rg	19.34 Å
Total atoms total_atoms	4852
Residues n_residues	313
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	62.6 Å
Rg (real space) rg_real	19.32 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.1540e+07
I(0) uncertainty (real space) i0_real_error	2.5640e+05
Rg (reciprocal space) rg_reciprocal	19.35 Å
I(0) (reciprocal space) i0_reciprocal	21540000.0000
Solution quality estimate total_estimate	0.8108
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.094
Kurtosis Kurtosis kurtosis	-0.481
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6509000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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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	Cell division cycle protein 20 homolog
Molecular weight formula_weight	34912.1 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	5295

GSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLWSASSGDILQLLQMEQPGEYISSVAWIKEGNYLAVGTSSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSYILSSGSRSGHIHHHDVRVAEHHVATLSGHSQEVCGLRWAPDGRHLASGGNDNLVNVWPSAPGEGGWVPLQTFTQHQGAVKAVAWCPWQSNVLATGGGTSDRHIRIWNVCSGACLSAVDAHSQVCSILWSPHYKELISGHGFAQNQLVIWKYPTMAKVAELKGHTSRVLSLTMSPDGATVASAAADETLRLWRCFELDP

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	443

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4ggca_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	4ggcA00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (4)

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Unit-cell length a length_a	41.281 Å
Unit-cell length b length_b	86.933 Å
Unit-cell length c length_c	48.339 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.350 Å
Low-resolution limit resolution_low	28.117 Å
R factor r_factor	0.1330
R_work r_work	0.1323
R_free r_free	0.1464

fit	/app/data/saxs_computation/gg/4ggc/4ggc.fit
pddf	/app/data/pr_computation/gg/4ggc/4ggc.pr.out
profile	/app/data/saxs_computation/gg/4ggc/4ggc.dat

Structural Analysis of Human Cdc20 Supports Multi-site Degron Recognition by APC/C

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

Cell division cycle protein 20 homolog

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