[English] 日本語
Yorodumi
- PDB-5tkm: Crystal structure of human APOBEC3B N-terminal Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tkm
TitleCrystal structure of human APOBEC3B N-terminal Domain
ComponentsDNA dC->dU-editing enzyme APOBEC-3B
KeywordsHYDROLASE / DEAMINASE / APOBEC
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / P-body ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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 dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXiao, X. / Yang, H. / Arutiunian, V. / Besse, G. / Morimoto, C. / Zirkle, B. / 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: Nucleic Acids Res. / Year: 2017
Title: Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation.
Authors: Xiao, X. / Yang, H. / Arutiunian, V. / Fang, Y. / Besse, G. / Morimoto, C. / Zirkle, B. / Chen, X.S.
History
DepositionOct 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / pdbx_audit_support / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3B
B: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2984
Polymers47,1672
Non-polymers1312
Water4,216234
1
A: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6492
Polymers23,5841
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6492
Polymers23,5841
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.739, 60.802, 111.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3


Mass: 23583.730 Da / Num. of mol.: 2 / Mutation: Y13D, Y28S, Y83D, W127S, Y146K, Y162D, Y191H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q9UH17, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01 M Iron (III) chloride hexahydrate, 0.1 M sodium citrate dehydrate pH 5.6, 10% v/v Jeffamine M-600

-
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: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33189 / % possible obs: 99.8 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 29.19

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K81

5k81


Resolution: 1.9→30.37 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.59
RfactorNum. reflection% reflection
Rfree0.2027 1993 6.02 %
Rwork0.1877 --
obs0.1886 33127 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 2 234 3368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073234
X-RAY DIFFRACTIONf_angle_d0.7934382
X-RAY DIFFRACTIONf_dihedral_angle_d15.4281174
X-RAY DIFFRACTIONf_chiral_restr0.053428
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8997-1.94720.29021350.23942098X-RAY DIFFRACTION97
1.9472-1.99980.26611440.22632212X-RAY DIFFRACTION100
1.9998-2.05860.23671400.21142183X-RAY DIFFRACTION100
2.0586-2.12510.251370.21632204X-RAY DIFFRACTION100
2.1251-2.2010.23771420.21442223X-RAY DIFFRACTION100
2.201-2.28910.24671380.1972187X-RAY DIFFRACTION100
2.2891-2.39320.22941420.20522221X-RAY DIFFRACTION100
2.3932-2.51930.18331470.20852213X-RAY DIFFRACTION100
2.5193-2.67710.21731420.1972229X-RAY DIFFRACTION100
2.6771-2.88360.19341410.19882263X-RAY DIFFRACTION100
2.8836-3.17360.17911430.18322230X-RAY DIFFRACTION100
3.1736-3.63210.19311410.17252246X-RAY DIFFRACTION100
3.6321-4.57360.17471500.15382283X-RAY DIFFRACTION100
4.5736-30.37340.2041510.19272342X-RAY DIFFRACTION97

+
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