[English] 日本語
Yorodumi
- PDB-4iou: Crystal structure of the HIV-1 Vif binding, catalytically active ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iou
TitleCrystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F
ComponentsDNA dC->dU-editing enzyme APOBEC-3F
KeywordsHYDROLASE / Catalytic Domain / Cytidine Deaminase / Cytidine deaminase-like / DNA binding / Cytidine deamination
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process ...apolipoprotein B mRNA editing enzyme complex / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of viral process / retrotransposon silencing / DNA demethylation / negative regulation of viral genome replication / positive regulation of defense response to virus by host / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / 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-3F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.751 Å
AuthorsBohn, M. / Shandilya, S.M.D. / Schiffer, C.A.
CitationJournal: Structure / Year: 2013
Title: Crystal Structure of the DNA Cytosine Deaminase APOBEC3F: The Catalytically Active and HIV-1 Vif-Binding Domain.
Authors: Bohn, M.F. / Shandilya, S.M. / Albin, J.S. / Kouno, T. / Anderson, B.D. / McDougle, R.M. / Carpenter, M.A. / Rathore, A. / Evans, L. / Davis, A.N. / Zhang, J. / Lu, Y. / Somasundaran, M. / ...Authors: Bohn, M.F. / Shandilya, S.M. / Albin, J.S. / Kouno, T. / Anderson, B.D. / McDougle, R.M. / Carpenter, M.A. / Rathore, A. / Evans, L. / Davis, A.N. / Zhang, J. / Lu, Y. / Somasundaran, M. / Matsuo, H. / Harris, R.S. / Schiffer, C.A.
History
DepositionJan 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references / Other / Refinement description
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 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: DNA dC->dU-editing enzyme APOBEC-3F
B: DNA dC->dU-editing enzyme APOBEC-3F
C: DNA dC->dU-editing enzyme APOBEC-3F
D: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1098
Polymers92,8484
Non-polymers2624
Water1,58588
1
A: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2772
Polymers23,2121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2772
Polymers23,2121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2772
Polymers23,2121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2772
Polymers23,2121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.790, 66.910, 75.640
Angle α, β, γ (deg.)110.75, 94.41, 108.83
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
DNA dC->dU-editing enzyme APOBEC-3F / Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F


Mass: 23211.936 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, UNP residues 185-373
Mutation: Y196D, H247G, C248R, C259A, F302D, W310K, Y314Y, Q315A, F363D, K355D, K358D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3F / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q8IUX4, 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl pH 8.0, 20% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2012 / Details: mirrors
RadiationMonochromator: GM/CA monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 22096 / Num. obs: 22560 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.5
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 31 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PHASERphasing
REFMAC5.7.0025refinement
HKL-2000data reduction
HKL-2000data scaling
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NYT

2nyt


Resolution: 2.751→36.457 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU ML: 0.31 / Isotropic thermal model: Isotropic / σ(F): 2 / Phase error: 24.65 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2326 1099 5.12 %
Rwork0.1934 --
obs0.1954 21463 95.97 %
all-22096 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-3.36 Å2-1.29 Å2
2---0.17 Å20.78 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.751→36.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 4 88 5661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035770
X-RAY DIFFRACTIONf_angle_d0.7657897
X-RAY DIFFRACTIONf_dihedral_angle_d15.3331877
X-RAY DIFFRACTIONf_chiral_restr0.052823
X-RAY DIFFRACTIONf_plane_restr0.0031018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7507-2.87580.31861180.2522449X-RAY DIFFRACTION92
2.8758-3.02740.27981490.2342598X-RAY DIFFRACTION97
3.0274-3.21690.26911370.21242547X-RAY DIFFRACTION97
3.2169-3.46510.28081230.19672582X-RAY DIFFRACTION97
3.4651-3.81350.21551480.17572542X-RAY DIFFRACTION96
3.8135-4.36460.18131310.17332572X-RAY DIFFRACTION97
4.3646-5.49590.22461570.16862531X-RAY DIFFRACTION96
5.4959-36.46020.22111360.20922543X-RAY DIFFRACTION96

+
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