7q46

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein

Method: X-RAY DIFFRACTION D_max: 103.6 Å Quality: EXCELLENT

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

E3 ubiquitin-protein ligase HERC2

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2941–3342	Not recorded	Pericentriolar material 1 protein × 1 （Q15154）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2941–3342	Not recorded	Pericentriolar material 1 protein × 1 （Q15154）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 2941–3342	Not recorded	Pericentriolar material 1 protein × 1 （Q15154） CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245

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 7Q46	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KEO Solution NMR structure of human protein HS00059, cytochrome-b5-like domain of the HERC2 E3 ligase. Northeast structural genomics consortium (NESG) target ht98a Deposited 2009-01-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1203–1296（94 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 300；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N] hs00059-1, 10 mM TRIS-2, 300 mM sodium chloride-3, 10 uM ZnSO4-4, 10 mM DTT-5, 0.01 % NaN3-6, 10 mM benzamidine-7, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3KCI The third RLD domain of HERC2 Deposited 2009-10-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3951–4321（371 aa） Fragment：UNP RESIDUES 3951-4321, RCC1-LIKE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290.9 K；20% PEG3350, 0.2mM MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.9K	Resolution 1.80 Å R-free 0.195
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03	Different construct 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 417–790（374 aa）	Not recorded	SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K	Resolution 2.60 Å R-free 0.238
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03	Different construct 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 417–790（374 aa）	Not recorded	SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K	Resolution 2.60 Å R-free 0.238
4L1M Structure of the first RCC1-like domain of HERC2 Deposited 2013-06-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 417–790（374 aa）	Not recorded	SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；1.5 M ammonium sulfate, 0.1 M Tris-hydrochloride, pH 8.5, vapor diffusion, temperature 291K	Resolution 2.60 Å R-free 0.238
6WW3 Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2702–2755（54 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000	Resolution 2.10 Å R-free 0.227
6WW3 Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2702–2755（54 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000	Resolution 2.10 Å R-free 0.227
6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2702–2751（50 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000	Resolution 2.25 Å R-free 0.243
6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2702–2751（50 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000	Resolution 2.25 Å R-free 0.243
7Q40 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.35 Å R-free 0.230
7Q40 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.35 Å R-free 0.230
7Q40 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 Deposited 2021-10-29	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.35 Å R-free 0.230
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2938–3342（405 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 3.01 Å R-free 0.255
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2938–3342（405 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 3.01 Å R-free 0.255
7Q41 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP) Deposited 2021-10-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；293.1500 hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 3.01 Å R-free 0.255
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2938–3342（405 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 1.95 Å R-free 0.206
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29	Different construct Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 1.95 Å R-free 0.206
7Q42 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B Deposited 2021-10-29	Different construct Different ligand/ion Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 1.95 Å R-free 0.206
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2941–3342（402 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.40 Å R-free 0.265
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2941–3342（402 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.40 Å R-free 0.265
7Q43 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 Deposited 2021-10-29	Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2941–3342（402 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.40 Å R-free 0.265
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2941–3342（402 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate	Resolution 2.20 Å R-free 0.231
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2941–3342（402 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate	Resolution 2.20 Å R-free 0.231
7Q44 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35 Deposited 2021-10-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2941–3342（402 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG 3350 0.18M tris amonium citrate	Resolution 2.20 Å R-free 0.231
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2938–3342（405 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.10 Å R-free 0.224
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29	Different construct Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.10 Å R-free 0.224
7Q45 Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1 Deposited 2021-10-29	Different construct Different ligand/ion Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2938–3342（405 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.10 Å R-free 0.224
7RGW Crystal structure of HERC2 DOC domain Deposited 2021-07-15	Different construct 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 2759–2914（156 aa） Fragment：DOC domain (UNP residues 2759-2914)	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M HEPES, pH 7.5, 25% PEG3350	Resolution 1.99 Å R-free 0.213
9L8Y Crystal structure of HERC2 Deposited 2024-12-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2539–2700（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；289 K；0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3,350	Resolution 1.92 Å R-free 0.206
9L93 Crystal structure of NCOA4 in complex with HERC2 Deposited 2024-12-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2539–2700（162 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 20% w/v Polyethylene glycol 4000	Resolution 1.73 Å R-free 0.207
9L93 Crystal structure of NCOA4 in complex with HERC2 Deposited 2024-12-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2539–2700（162 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 20% w/v Polyethylene glycol 4000	Resolution 1.73 Å R-free 0.207

14 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HERC2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–405； UniProt 2941–3342 Author chain C； PDBConstruct 4–405； UniProt 2941–3342 Author chain E； PDBConstruct 4–405； UniProt 2941–3342

Pericentriolar material 1 protein

OrganismNot specified

UniProt Q15154

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1737–1751	Not recorded	E3 ubiquitin-protein ligase HERC2 × 1 （O95714）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1737–1751	Not recorded	E3 ubiquitin-protein ligase HERC2 × 1 （O95714）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 1737–1751	Not recorded	E3 ubiquitin-protein ligase HERC2 × 1 （O95714） CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；hanging drop 20% PEG 3350 0.18M tris amonium citrate	Resolution 2.46 Å R-free 0.245

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7Q46	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6HYL Structure of PCM1 LIR motif bound to GABARAP Deposited 2018-10-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1959–1972（14 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M CaCl2, 0.1 M HEPES pH 7, 20% w/v PEG 6000	Resolution 1.56 Å R-free 0.247
6HYL Structure of PCM1 LIR motif bound to GABARAP Deposited 2018-10-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1959–1972（14 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M CaCl2, 0.1 M HEPES pH 7, 20% w/v PEG 6000	Resolution 1.56 Å R-free 0.247
6HYM Structure of PCM1 LIR motif bound to GABARAP Deposited 2018-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1959–1972（14 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% w/v PEG 1500, 0.1 M SPG pH 8.5	Resolution 1.86 Å R-free 0.217
6HYM Structure of PCM1 LIR motif bound to GABARAP Deposited 2018-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1959–1972（14 aa）	Not recorded	GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% w/v PEG 1500, 0.1 M SPG pH 8.5	Resolution 1.86 Å R-free 0.217

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PCM1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–15； UniProt 1737–1751 Author chain D； PDBConstruct 1–15； UniProt 1737–1751 Author chain F； PDBConstruct 1–15； UniProt 1737–1751

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7q46
Deposition date deposition_date	2021-10-29
Structure title title	Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein
Keywords keywords	;7-bladed beta-propeller HERC2 RCC1-like Domain 2 RLD2 ubiquitin ligase PCM1 pericentriolar material 1 protein DXDKDED motif, PROTEIN BINDING ;; PROTEIN BINDING
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	33.93 Å
Radius of gyration Rg (electron density) rg_electron	33.70 Å
Forward intensity I(0) i0	233119000.00
Molecular weight molecular_weight	119770.0 kDa
Excluded volume excluded_volume	148760 Å³
Envelope volume envelope_volume	178620 Å³
Hydration-shell volume shell_volume	43688 Å³
Envelope diameter envelope_diameter	106.8 Å
Shell Rg shell_rg	40.49 Å
Envelope Rg envelope_rg	33.55 Å
Shape Rg shape_rg	33.66 Å
Total Rg total_rg	34.28 Å
Total atoms total_atoms	8427
Residues n_residues	1128
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	103.6 Å
Rg (real space) rg_real	33.84 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	2.3310e+08
I(0) uncertainty (real space) i0_real_error	3.5790e+06
Rg (reciprocal space) rg_reciprocal	33.90 Å
I(0) (reciprocal space) i0_reciprocal	233100000.0000
Solution quality estimate total_estimate	0.9045
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.3 Å
Skewness Skewness skewness	0.131
Kurtosis Kurtosis kurtosis	-0.750
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	60540000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.872

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase HERC2
Molecular weight formula_weight	42770.6 kDa
EC 编号 ec_number	2.3.2.26
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	8899

GAMGSLIRKKAAGLESAATIRTKVFVWGLNDKDQLGGLKGSKIKVPSFSETLSALNVVQVAGGSKSLFAVTVEGKVYACGEATNGRLGLGISSGTVPIPRQITALSSYVVKKVAVHSGGRHATALTVDGKVFSWGEGDDGKLGHFSRMNCDKPRLIEALKTKRIRDIACGSSHSAALTSSGELYTWGLGEYGRLGHGDNTTQLKPKMVKVLLGHRVIQVACGSRDAQTLALTDEGLVFSWGDGDFGKLGRGGSEGCNIPQNIERLNGQGVCQIECGAQFSLALTKSGVVWTWGKGDYFRLGHGSDVHVRKPQVVEGLRGKKIVHVAVGALHCLAVTDSGQVYAWGDNDHGQQGNGTTTVNRKPTLVQGLEGQKITRVACGSSHSVAWTTVDVATPSVHEPVLFQT

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 polymer

Description description	Pericentriolar material 1 protein
Molecular weight formula_weight	1783.8 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,B

DEDKDKDETETVKQT

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	461

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8. Citations (1)

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Unit-cell length a length_a	107.660 Å
Unit-cell length b length_b	107.660 Å
Unit-cell length c length_c	241.210 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	24

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

Resolution resolution	2.460 Å
Low-resolution limit resolution_low	49.156 Å
R factor r_factor	0.1820
R_work r_work	0.1786
R_free r_free	0.2453

fit	/app/data/saxs_computation/q4/7q46/7q46.fit
pddf	/app/data/pr_computation/q4/7q46/7q46.pr.out
profile	/app/data/saxs_computation/q4/7q46/7q46.dat

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein

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

E3 ubiquitin-protein ligase HERC2

State in the Current Structure

Other States of the Same Protein in the Database

Pericentriolar material 1 protein

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)