SAXSdb — 4ap4

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

E3 UBIQUITIN LIGASE RNF4

RATTUS NORVEGICUS

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 131–194 Chain A； UniProt 131–194	Fragment：RESIDUES 131-195,131-195	UBIQUITIN-CONJUGATING ENZYME E2 D1 × 2 （P51668） UBIQUITIN C × 2 （F5H7Y5） ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；pH 7.2	Resolution 2.21 Å R-free 0.242

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 4AP4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3NG2 Crystal structure of the RNF4 ring domain dimer Deposited 2010-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 124–194（71 aa） Fragment：RING domain Chain B 124–194（71 aa） Fragment：RING domain	Not recorded	ZN ZINC ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；0.2M lithium sulfate, 0.1M bis-Tris, 22% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.242
5AIT A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 131–194（64 aa） Fragment：RING DOMAIN, UNP RESIDUES 131-194,131-194	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.40 Å R-free 0.286
5AIU A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 131–194（64 aa） Fragment：RING DOMAIN, UNP RESIDUES 131-194,131-194	Mutation：YES	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions 1,2-ETHANEDIOL	Resolution 2.21 Å R-free 0.255

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RNF4_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–68； UniProt 131–194 Author chain A； PDBConstruct 70–133； UniProt 131–194

UBIQUITIN-CONJUGATING ENZYME E2 D1

HOMO SAPIENS

UniProt P51668

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain B； UniProt 1–147 Chain E； UniProt 1–147	Mutation：YES	E3 UBIQUITIN LIGASE RNF4 × 1 （O88846） UBIQUITIN C × 2 （F5H7Y5） ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；pH 7.2	Resolution 2.21 Å R-free 0.242

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 4AP4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2C4P Crystal structure of human ubiquitin-conjugating enzyme UbcH5A Deposited 2005-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–147（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；200 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000	Resolution 2.35 Å R-free 0.272
2C4P Crystal structure of human ubiquitin-conjugating enzyme UbcH5A Deposited 2005-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–147（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；200 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000	Resolution 2.35 Å R-free 0.272
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa）	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000	Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–147（147 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000	Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–147（147 aa）	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000	Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–147（147 aa）	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000	Resolution 2.10 Å R-free 0.233
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–147（147 aa） Fragment：Ubiquitin-conjugating enzyme E2 D1	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K	Resolution 3.40 Å R-free 0.319
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–147（147 aa） Fragment：Ubiquitin-conjugating enzyme E2 D1	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K	Resolution 3.40 Å R-free 0.319
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02	Different construct Different mutation/modification 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 1–147（147 aa） Fragment：E2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.275
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02	Different construct Different mutation/modification 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 1–147（147 aa） Fragment：E2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.275
4QPL Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex Deposited 2014-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa）	Not recorded	V3L 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.8 M sodium citrate, 80 mM Tris HCl pH7.0, 160 mM NaCl, 4 mMDTT, 20 mM trimethylamin HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.222
4QPL Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex Deposited 2014-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–147（147 aa）	Not recorded	V3L 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.8 M sodium citrate, 80 mM Tris HCl pH7.0, 160 mM NaCl, 4 mMDTT, 20 mM trimethylamin HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.222
5FER Complex of TRIM25 RING with UbcH5-Ub Deposited 2015-12-17	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–147（147 aa） Chain E 1–147（147 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；10% PEG 20000 and 100 mM Tris pH 8.5	Resolution 2.34 Å R-free 0.273
5TUT UbcH5a-Ub isopeptide conjugate Deposited 2016-11-07	Different construct Different mutation/modification 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 1–147（147 aa）	Mutation：C85K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；Hampton PEG/Ion F10	Resolution 2.60 Å R-free 0.243
6D4P Ube2D1 in complex with ubiquitin variant Ubv.D1.1 Deposited 2018-04-18	Different construct Different mutation/modification 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 1–147（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；24% PEG2000-MME, 0.2M trimethylamine N-oxide, 0.1M Tris-HCl	Resolution 2.11 Å R-free 0.231
7ZJ3 Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate Deposited 2022-04-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 2–146（145 aa） Chain K 2–146（145 aa）	Mutation：S22R C85K Mutation：S22R C85K	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5 10% (w/v) PEG 8K	Resolution 2.53 Å R-free 0.258
7ZJ3 Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate Deposited 2022-04-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 2–146（145 aa） Chain H 2–146（145 aa）	Mutation：S22R C85K Mutation：S22R C85K	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5 10% (w/v) PEG 8K	Resolution 2.53 Å R-free 0.258
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07	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 × 8 PDB declaration: octameric	Chain D 2–147（146 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17	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 × 8 PDB declaration: octameric	Chain D 2–147（146 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.69 Å
9V0B Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17	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 × 8 PDB declaration: octameric	Chain D 2–147（146 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.54 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17	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 × 8 PDB declaration: octameric	Chain D 2–147（146 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.71 Å

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UB2D1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–153； UniProt 1–147 Author chain E； PDBConstruct 7–153； UniProt 1–147

UBIQUITIN C

HOMO SAPIENS

UniProt F5H7Y5

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain C； UniProt 76–152 Chain F； UniProt 76–152	Fragment：RESIDUES 76-152	E3 UBIQUITIN LIGASE RNF4 × 1 （O88846） UBIQUITIN-CONJUGATING ENZYME E2 D1 × 2 （P51668） ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；pH 7.2	Resolution 2.21 Å R-free 0.242

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	F5H7Y5_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–80； UniProt 76–152 Author chain F； PDBConstruct 4–80； UniProt 76–152

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	4ap4
Deposition date deposition_date	2012-03-30
Structure title title	Rnf4 - ubch5a - ubiquitin heterotrimeric complex
Keywords keywords	LIGASE-SIGNALLING PROTEIN COMPLEX, CHIMERA; LIGASE/SIGNALLING PROTEIN
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	31.27 Å
Radius of gyration Rg (electron density) rg_electron	31.26 Å
Forward intensity I(0) i0	69847300.00
Molecular weight molecular_weight	65527.0 kDa
Excluded volume excluded_volume	81915 Å³
Envelope volume envelope_volume	102580 Å³
Hydration-shell volume shell_volume	29752 Å³
Envelope diameter envelope_diameter	116.0 Å
Shell Rg shell_rg	35.18 Å
Envelope Rg envelope_rg	31.31 Å
Shape Rg shape_rg	31.36 Å
Total Rg total_rg	31.30 Å
Total atoms total_atoms	4585
Residues n_residues	580
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	110.2 Å
Rg (real space) rg_real	31.67 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	6.9850e+07
I(0) uncertainty (real space) i0_real_error	1.0390e+06
Rg (reciprocal space) rg_reciprocal	31.51 Å
I(0) (reciprocal space) i0_reciprocal	69840000.0000
Solution quality estimate total_estimate	0.7832
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.2 Å
Skewness Skewness skewness	0.631
Kurtosis Kurtosis kurtosis	-0.147
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13150000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.627; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.589; Smooth: 0.707

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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	E3 UBIQUITIN LIGASE RNF4
Molecular weight formula_weight	14758.2 kDa
EC 编号 ec_number	6.3.2.-
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	4748

GAMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI

来源 Source

来源生物 organism	RATTUS NORVEGICUS
通用名 common_name	NORWAY RAT
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	UBIQUITIN-CONJUGATING ENZYME E2 D1
Molecular weight formula_weight	17134.6 kDa
EC 编号 ec_number	6.3.2.19
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

GAGSGSMALKRIQKELSDLQRDPPAHCRAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM

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	UBIQUITIN C
Molecular weight formula_weight	8893.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAMGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d4ap4b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d4ap4b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ap4c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d4ap4e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d4ap4f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (5 domains)

Domain ID domain_id	4ap4A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	4ap4B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	4ap4C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4ap4E00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	4ap4F00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	50.480 Å
Unit-cell length b length_b	65.090 Å
Unit-cell length c length_c	189.650 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.210 Å
Low-resolution limit resolution_low	94.820 Å
R factor r_factor	0.2093
R_work r_work	0.2075
R_free r_free	0.2417

fit	/app/data/saxs_computation/ap/4ap4/4ap4.fit
pddf	/app/data/pr_computation/ap/4ap4/4ap4.pr.out
profile	/app/data/saxs_computation/ap/4ap4/4ap4.dat

Rnf4 - ubch5a - ubiquitin heterotrimeric complex

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

E3 UBIQUITIN LIGASE RNF4

State in the Current Structure

Other States of the Same Protein in the Database

UBIQUITIN-CONJUGATING ENZYME E2 D1

State in the Current Structure

Other States of the Same Protein in the Database

UBIQUITIN C

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

6. Entities and Polymers Entities & Polymers (5)

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

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)