[English] 日本語
Yorodumi
- PDB-7uu5: Crystal structure of APOBEC3G complex with 5'-Overhang dsRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uu5
TitleCrystal structure of APOBEC3G complex with 5'-Overhang dsRNA
Components
  • DNA dC->dU-editing enzyme APOBEC-3G
  • RNA (5'-R(P*UP*AP*AP*CP*CP*GP*CP*AP*GP*CP*G)-3')
  • RNA (5'-R(P*UP*AP*AP*CP*GP*CP*UP*GP*CP*GP*G)-3')
KeywordsHYDROLASE/RNA / Deaminase / APOBEC / HYDROLASE / HYDROLASE-RNA complex
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 / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / zinc ion binding / nucleus
Similarity search - Function
Novel AID APOBEC clade 2 / : / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYang, H. / Li, S. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI150524 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G.
Authors: Yang, H. / Kim, K. / Li, S. / Pacheco, J. / Chen, X.S.
History
DepositionApr 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3G
B: DNA dC->dU-editing enzyme APOBEC-3G
M: RNA (5'-R(P*UP*AP*AP*CP*GP*CP*UP*GP*CP*GP*G)-3')
N: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*CP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8328
Polymers101,5704
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.305, 71.559, 72.710
Angle α, β, γ (deg.)119.390, 111.000, 90.080
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 14 or resid 16...
21(chain B and (resid 3 through 14 or resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 14 or resid 16...A3 - 14
121(chain A and (resid 3 through 14 or resid 16...A16 - 58
131(chain A and (resid 3 through 14 or resid 16...A60 - 98
141(chain A and (resid 3 through 14 or resid 16...A100 - 172
151(chain A and (resid 3 through 14 or resid 16...A1 - 383
161(chain A and (resid 3 through 14 or resid 16...A255 - 3
171(chain A and (resid 3 through 14 or resid 16...A320 - 354
181(chain A and (resid 3 through 14 or resid 16...A1 - 383
191(chain A and (resid 3 through 14 or resid 16...A356 - 383
1101(chain A and (resid 3 through 14 or resid 16...A800 - 900
211(chain B and (resid 3 through 14 or resid 16...B3 - 14
221(chain B and (resid 3 through 14 or resid 16...B16 - 58
231(chain B and (resid 3 through 14 or resid 16...B60 - 98
241(chain B and (resid 3 through 14 or resid 16...B100 - 172
251(chain B and (resid 3 through 14 or resid 16...B174 - 215
261(chain B and (resid 3 through 14 or resid 16...B0
271(chain B and (resid 3 through 14 or resid 16...B1 - 383
281(chain B and (resid 3 through 14 or resid 16...B320 - 354
291(chain B and (resid 3 through 14 or resid 16...B356 - 3
2101(chain B and (resid 3 through 14 or resid 16...B356 - 383
2111(chain B and (resid 3 through 14 or resid 16...B800 - 900

-
Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3G / Deoxycytidine deaminase


Mass: 45130.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: APOBEC3G / Production host: Escherichia coli (E. coli)
References: UniProt: M1GSK9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: RNA chain RNA (5'-R(P*UP*AP*AP*CP*GP*CP*UP*GP*CP*GP*G)-3')


Mass: 5663.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*UP*AP*AP*CP*CP*GP*CP*AP*GP*CP*G)-3')


Mass: 5646.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Na/K phosphate, pH 6.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 21497 / % possible obs: 98.2 % / Redundancy: 3.3 % / CC1/2: 0.994 / Net I/σ(I): 11.56
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 2116 / CC1/2: 0.845

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P3X

6p3x


Resolution: 2.9→46.508 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 1335 6.26 %
Rwork0.187 20006 -
obs0.1907 21341 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 250.37 Å2 / Biso mean: 86.8796 Å2 / Biso min: 32.4 Å2
Refinement stepCycle: final / Resolution: 2.9→46.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 471 4 0 6771
Biso mean--113.64 --
Num. residues----780
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3441X-RAY DIFFRACTION12.946TORSIONAL
12B3441X-RAY DIFFRACTION12.946TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-3.00360.39471390.2965184392
3.0036-3.12390.31871320.2574200798
3.1239-3.2660.28551260.231200999
3.266-3.43820.32961420.2175201399
3.4382-3.65350.25591320.1945203299
3.6535-3.93540.23391460.1803198199
3.9354-4.33120.23251260.1694203099
4.3312-4.95730.22831360.1538200899
4.9573-6.24330.21421250.1852205999
6.2433-46.5080.20221310.1707202499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5612-0.8205-1.45362.850.86352.28780.09740.10460.2114-0.085-0.20680.3538-0.2566-0.33450.09920.4386-0.0318-0.07480.4335-0.02460.3709-42.16.010824.8174
24.0274-1.2030.6381.45530.08131.24720.18880.2046-0.1232-0.0555-0.0367-0.26120.1654-0.0386-0.16970.5178-0.00660.01490.44760.02150.5556-13.3212-8.26825.1593
33.93290.2281-1.42343.0246-0.61912.30970.18350.08960.1912-0.0541-0.1637-0.37-0.24280.1645-0.03190.43740.022-0.04580.487-0.06740.361-16.06744.5335-19.8691
44.12780.76540.92211.3887-0.1841.10150.0845-0.1617-0.11240.1116-0.03910.38060.1659-0.0269-0.06590.48920.00770.00210.4257-0.08080.5616-46.7534-8.4703-20.565
55.553-1.949-0.47575.8904-1.47443.00640.37950.21291.8982-1.31440.6976-0.7272-2.0308-0.4415-1.06351.76820.06020.41591.24320.30911.0893-28.319817.25111.7125
66.04451.07230.0567.84373.74893.20740.3704-0.36911.98551.3280.48680.5995-1.39220.6681-0.92031.561-0.08870.37161.3345-0.22541.1158-29.520117.2583.0656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 141 )A1 - 141
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 383 )A142 - 383
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 164 )B1 - 164
4X-RAY DIFFRACTION4chain 'B' and (resid 165 through 383 )B165 - 383
5X-RAY DIFFRACTION5chain 'M' and (resid 2 through 12 )M2 - 12
6X-RAY DIFFRACTION6chain 'N' and (resid 2 through 12 )N2 - 12

+
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