SAXSdb — 3ffl

▼

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

Anaphase-promoting complex subunit 7

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–147 Chain C； UniProt 1–147	Fragment：N-terminal domain Mutation：M49L, M128L, M134V, M160L	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.2M sodium/potassium tartrate, 15% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.50 Å R-free 0.240
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–147 Chain D； UniProt 1–147	Fragment：N-terminal domain Mutation：M49L, M128L, M134V, M160L	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.2M sodium/potassium tartrate, 15% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.50 Å R-free 0.240

Other States of the Same Protein in the Database

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

Other PDB	Difference from Current Entry 3FFL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4UI9 Atomic structure of the human Anaphase-Promoting Complex Deposited 2015-03-27	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 X 35–599（565 aa） Chain Y 35–599（565 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
5A31 Structure of the human APC-Cdh1-Hsl1-UbcH10 complex. Deposited 2015-05-26	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 × 24 PDB declaration: 24-meric	Chain X 1–599（599 aa） Chain Y 1–599（599 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
5G04 Structure of the human APC-Cdc20-Hsl1 complex Deposited 2016-03-16	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 × 21 PDB declaration: 21-meric	Chain X 1–599（599 aa） Chain Y 1–599（599 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
5G05 Cryo-EM structure of combined apo phosphorylated APC Deposited 2016-03-16	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 × 20 PDB declaration: eicosameric	Chain X 1–599（599 aa） Chain Y 1–599（599 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 3.40 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain X 35–599（565 aa） Chain Y 35–599（565 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 experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain X 35–599（565 aa） Chain Y 35–599（565 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
5L9T Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density Deposited 2016-06-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 22 PDB declaration: 22-meric	Chain X 35–599（565 aa） Chain Y 35–599（565 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.40 Å
5L9U Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with a cross linked Ubiquitin variant-substrate-UBE2C (UBCH10) complex representing key features of multiubiquitination Deposited 2016-06-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 22 PDB declaration: 22-meric	Chain X 35–599（565 aa） Chain Y 35–599（565 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.40 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 experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain X 1–599（599 aa） Chain Y 1–599（599 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
6Q6G Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D1 box class Deposited 2018-12-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain Y 1–599（599 aa） Chain Z 1–599（599 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain Y 1–599（599 aa） Chain Z 1–599（599 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 experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain X 1–599（599 aa） Chain Y 1–599（599 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
6TM5 Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution Deposited 2019-12-03	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 × 22 PDB declaration: 22-meric	Chain X 1–599（599 aa） Chain Y 1–599（599 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6TNT SUMOylated apoAPC/C with repositioned APC2 WHB domain Deposited 2019-12-10	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 × 20 PDB declaration: eicosameric	Chain X 1–599（599 aa） Chain Y 1–599（599 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.78 Å
8PKP Cryo-EM structure of the apo Anaphase-promoting complex/cyclosome (APC/C) at 3.2 Angstrom resolution Deposited 2023-06-27	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 × 19 PDB declaration: 19-meric	Chain Y 1–565（565 aa） Chain Z 1–565（565 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8TAR APC/C-CDH1-UBE2C-Ubiquitin-CyclinB-NTD Deposited 2023-06-27	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 × 22 PDB declaration: 22-meric	Chain Y 35–599（565 aa） Chain Z 35–599（565 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8TAU APC/C-CDH1-UBE2C-UBE2S-Ubiquitin-CyclinB Deposited 2023-06-27	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 Y 35–599（565 aa） Chain Z 35–599（565 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9GAW High-resolution structure of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-activator Cdh1 Deposited 2024-07-29	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 × 21 PDB declaration: 21-meric	Chain Y 1–599（599 aa） Chain Z 1–599（599 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9N9R Model of APC/C-CDC20-UBE2C from H2A/H2B-bound complex Deposited 2025-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain Y 35–599（565 aa） Chain Z 35–599（565 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 mutation/modification 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 Y 35–599（565 aa） Chain Z 35–599（565 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APC7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–167； UniProt 1–147 Author chain B； PDBConstruct 21–167； UniProt 1–147 Author chain C； PDBConstruct 21–167； UniProt 1–147 Author chain D； PDBConstruct 21–167； UniProt 1–147

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ffl
Deposition date deposition_date	2008-12-03
Structure title title	Crystal Structure of the N-terminal Domain of Anaphase-Promoting Complex Subunit 7
Keywords keywords	Tetratricopeptide repeat motif, helis-turn-helix, Cell cycle, Cell division, Mitosis, TPR repeat, Ubl conjugation pathway; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	36.38 Å
Radius of gyration Rg (electron density) rg_electron	36.71 Å
Forward intensity I(0) i0	48243300.00
Molecular weight molecular_weight	56897.0 kDa
Excluded volume excluded_volume	72137 Å³
Envelope volume envelope_volume	102200 Å³
Hydration-shell volume shell_volume	25707 Å³
Envelope diameter envelope_diameter	129.7 Å
Shell Rg shell_rg	38.50 Å
Envelope Rg envelope_rg	36.21 Å
Shape Rg shape_rg	36.69 Å
Total Rg total_rg	36.92 Å
Total atoms total_atoms	3997
Residues n_residues	500
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

▼

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

Maximum dimension Dmax dmax	124.7 Å
Rg (real space) rg_real	36.76 Å
Rg uncertainty (real space) rg_real_error	1.28 Å
I(0) (real space) i0_real	4.8240e+07
I(0) uncertainty (real space) i0_real_error	8.7310e+05
Rg (reciprocal space) rg_reciprocal	36.53 Å
I(0) (reciprocal space) i0_reciprocal	48230000.0000
Solution quality estimate total_estimate	0.7925
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.402
Kurtosis Kurtosis kurtosis	-0.676
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3781000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.369; Smooth: 0.901

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3fflA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3fflB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3fflC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	3fflD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	80.493 Å
Unit-cell length b length_b	64.076 Å
Unit-cell length c length_c	81.597 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	41.000 Å
R factor r_factor	0.2177
R_work r_work	0.2165
R_free r_free	0.2401

Description description	Anaphase-promoting complex subunit 7
Molecular weight formula_weight	18714.5 kDa
Mutation mutation	M49L, M128L, M134V, M160L
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4045

Crystal Structure of the N-terminal Domain of Anaphase-Promoting Complex Subunit 7

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

Anaphase-promoting complex subunit 7

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

fit	/app/data/saxs_computation/ff/3ffl/3ffl.fit
pddf	/app/data/pr_computation/ff/3ffl/3ffl.pr.out
profile	/app/data/saxs_computation/ff/3ffl/3ffl.dat