[English] 日本語
Yorodumi
- PDB-5k83: Crystal Structure of a Primate APOBEC3G N-Domain, in Complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k83
TitleCrystal Structure of a Primate APOBEC3G N-Domain, in Complex with ssDNA
Components
  • Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
KeywordsHYDROLASE / APOBEC3G / Vif / HIV / APOBEC
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / DNA cytosine deamination / cytidine deaminase activity / transposable element silencing / negative regulation of viral genome replication / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / zinc ion binding / nucleus
Similarity search - Function
Novel AID APOBEC clade 2 / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
DNA / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsXiao, X. / Li, S.-X. / Yang, H. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087986 United States
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structures of APOBEC3G N-domain alone and its complex with DNA.
Authors: Xiao, X. / Li, S.X. / Yang, H. / Chen, X.S.
History
DepositionMay 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _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
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
C: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
I: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
F: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
E: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
J: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
B: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
A: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
H: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,94015
Polymers147,5489
Non-polymers3926
Water4,972276
1
D: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
C: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
I: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3135
Polymers49,1833
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
E: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
J: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3135
Polymers49,1833
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
A: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
H: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3135
Polymers49,1833
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.720, 83.311, 105.754
Angle α, β, γ (deg.)90.000, 120.000, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G


Mass: 23092.783 Da / Num. of mol.: 6
Fragment: UNP residues 1-195 (139CQKRDGPH146 replaced by AEAG)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: APOBEC3G / Plasmid: pGEX-6P-1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: M1GSK9
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2996.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Macaca mulatta (Rhesus monkey)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.0, 6% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→45.792 Å / Num. obs: 63261 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 26
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K81

5k81


Resolution: 2.39→45.792 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7
RfactorNum. reflection% reflection
Rfree0.2509 1990 3.15 %
Rwork0.1865 --
obs0.1885 63249 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.32 Å2 / Biso mean: 45.3537 Å2 / Biso min: 14.32 Å2
Refinement stepCycle: final / Resolution: 2.39→45.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9454 101 107 276 9938
Biso mean--60.88 41.66 -
Num. residues----1127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099894
X-RAY DIFFRACTIONf_angle_d1.16913461
X-RAY DIFFRACTIONf_chiral_restr0.0471373
X-RAY DIFFRACTIONf_plane_restr0.0061684
X-RAY DIFFRACTIONf_dihedral_angle_d15.5743671
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3871-2.44680.31031330.24064239437296
2.4468-2.51290.29471470.22743214468100
2.5129-2.58680.23841470.20343974544100
2.5868-2.67030.24381370.193343144451100
2.6703-2.76580.30391360.207743314467100
2.7658-2.87650.28611440.211744234567100
2.8765-3.00740.2951410.203343714512100
3.0074-3.16590.19491440.202643304474100
3.1659-3.36420.33261320.213644234555100
3.3642-3.62380.29021470.199843614508100
3.6238-3.98830.26221530.184944054558100
3.9883-4.5650.19851470.167743934540100
4.565-5.74960.25721320.163844404572100
5.7496-45.80030.18831500.149845114661100

+
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