[English] 日本語
Yorodumi
- PDB-4o2w: Crystal structure of the third RCC1-like domain of HERC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o2w
TitleCrystal structure of the third RCC1-like domain of HERC1
ComponentsE3 ubiquitin-protein ligase HERC1
KeywordsLIGASE / RCC1 / RLD / beta-propeller / HERC1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cerebellar Purkinje cell differentiation / corpus callosum development / HECT-type E3 ubiquitin transferase / neuromuscular process controlling balance / guanyl-nucleotide exchange factor activity / negative regulation of autophagy / autophagy / ubiquitin-protein transferase activity / neuron projection development / Antigen processing: Ubiquitination & Proteasome degradation ...cerebellar Purkinje cell differentiation / corpus callosum development / HECT-type E3 ubiquitin transferase / neuromuscular process controlling balance / guanyl-nucleotide exchange factor activity / negative regulation of autophagy / autophagy / ubiquitin-protein transferase activity / neuron projection development / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / Golgi apparatus / membrane / cytosol / cytoplasm
Similarity search - Function
HERC1, SPRY domain / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) ...HERC1, SPRY domain / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Concanavalin A-like lectin/glucanase domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Probable E3 ubiquitin-protein ligase HERC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDong, A. / Hu, J. / Li, Y. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the third RCC1-like domain of HERC1
Authors: Hu, J. / Dong, A. / Li, Y. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HERC1
B: E3 ubiquitin-protein ligase HERC1
C: E3 ubiquitin-protein ligase HERC1
D: E3 ubiquitin-protein ligase HERC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,95337
Polymers171,7034
Non-polymers25033
Water12,124673
1
A: E3 ubiquitin-protein ligase HERC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,05610
Polymers42,9261
Non-polymers1319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase HERC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,95011
Polymers42,9261
Non-polymers2410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: E3 ubiquitin-protein ligase HERC1


Theoretical massNumber of molelcules
Total (without water)42,9264
Polymers42,9261
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: E3 ubiquitin-protein ligase HERC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,02112
Polymers42,9261
Non-polymers9511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.383, 70.902, 105.549
Angle α, β, γ (deg.)70.930, 81.260, 90.840
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
E3 ubiquitin-protein ligase HERC1 / HECT domain and RCC1-like domain-containing protein 1 / p532 / p619


Mass: 42925.789 Da / Num. of mol.: 4 / Fragment: UNP residues 3975-4360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HERC1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R
References: UniProt: Q15751, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 25 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 1500, 0.2 M Magnesium Choride, 0.1 M Hepes pH7.5, vapor diffusion hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 97126 / Num. obs: 97126 / % possible obs: 100 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 7.1
Reflection shellHighest resolution: 2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 1.53 / Num. unique all: 4850 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
PHASER2.5.5phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KCI

3kci


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2077 / WRfactor Rwork: 0.1716 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8318 / SU B: 4.705 / SU ML: 0.128 / SU R Cruickshank DPI: 0.174 / SU Rfree: 0.1543 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 980 1 %RANDOM
Rwork0.1813 ---
obs0.1817 97125 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.16 Å2 / Biso mean: 19.6993 Å2 / Biso min: 4.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å2-0.02 Å2-0.15 Å2
2--0.59 Å20.19 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10636 0 33 673 11342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910965
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210225
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.93414888
X-RAY DIFFRACTIONr_angle_other_deg0.774323446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73651496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99524.722468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.782151696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3371555
X-RAY DIFFRACTIONr_chiral_restr0.0770.21650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022613
X-RAY DIFFRACTIONr_mcbond_it0.9881.845888
X-RAY DIFFRACTIONr_mcbond_other0.9871.845887
X-RAY DIFFRACTIONr_mcangle_it1.6262.7567368
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 78 -
Rwork0.239 6829 -
all-6907 -
obs--95.39 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more