[English] 日本語
Yorodumi
- PDB-7uu3: Crystal structure of APOBEC3G complex with 3'overhangs RNA-Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uu3
TitleCrystal structure of APOBEC3G complex with 3'overhangs RNA-Complex
Components
  • DNA dC->dU-editing enzyme APOBEC-3G
  • RNA (5'-R(*CP*CP*CP*AP*CP*GP*GP*GP*AP*AP*U)-3')
  • RNA (5'-R(*CP*CP*CP*GP*UP*GP*GP*GP*AP*AP*U)-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 / 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 / : / 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: 3.099 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
C: RNA (5'-R(*CP*CP*CP*AP*CP*GP*GP*GP*AP*AP*U)-3')
D: RNA (5'-R(*CP*CP*CP*GP*UP*GP*GP*GP*AP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4158
Polymers99,1534
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-164 kcal/mol
Surface area39610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.709, 67.192, 79.624
Angle α, β, γ (deg.)98.290, 108.720, 112.660
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 60 or resid 65...
21(chain B and (resid 8 through 60 or resid 65...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 8 through 60 or resid 65...A8 - 60
121(chain A and (resid 8 through 60 or resid 65...A65 - 71
131(chain A and (resid 8 through 60 or resid 65...A73 - 194
141(chain A and (resid 8 through 60 or resid 65...A196
151(chain A and (resid 8 through 60 or resid 65...A330
161(chain A and (resid 8 through 60 or resid 65...A330 - 806
211(chain B and (resid 8 through 60 or resid 65...B8 - 60
221(chain B and (resid 8 through 60 or resid 65...B65 - 71
231(chain B and (resid 8 through 60 or resid 65...B73 - 194
241(chain B and (resid 8 through 60 or resid 65...B196
251(chain B and (resid 8 through 60 or resid 65...B330
261(chain B and (resid 8 through 60 or resid 65...B330 - 806

-
Components

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


Mass: 45144.473 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(*CP*CP*CP*AP*CP*GP*GP*GP*AP*AP*U)-3')


Mass: 4423.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*CP*CP*CP*GP*UP*GP*GP*GP*AP*AP*U)-3')


Mass: 4440.651 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.1 M MES, pH 6.3, 12% PEG 20K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.099→50 Å / Num. obs: 61081 / % possible obs: 98.24 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 8.89
Reflection shellResolution: 3.099→3.21 Å / Redundancy: 2.4 % / Num. unique obs: 4248 / CC1/2: 0.557 / % possible all: 93.7

-
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: 3.099→45.695 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 1868 10.01 %
Rwork0.1698 16800 -
obs0.1739 18668 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.74 Å2 / Biso mean: 94.3458 Å2 / Biso min: 41.2 Å2
Refinement stepCycle: final / Resolution: 3.099→45.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 465 4 0 6607
Biso mean--83.97 --
Num. residues----761
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3550X-RAY DIFFRACTION5.912TORSIONAL
12B3550X-RAY DIFFRACTION5.912TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.099-3.18260.36631360.295122492
3.1826-3.27620.29031400.2774126498
3.2762-3.38190.34061460.2391130998
3.3819-3.50270.24471400.2172126499
3.5027-3.64290.23761450.2129129799
3.6429-3.80860.23771460.1995132099
3.8086-4.00930.23321450.2034129599
4.0093-4.26030.2021440.1648129499
4.2603-4.5890.18221460.1446132099
4.589-5.05030.18121460.1397131199
5.0503-5.77980.2111430.1558128799
5.7798-7.27720.22661460.1662130999
7.2772-45.6950.14751450.1202130699
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)
11.01110.2002-0.28790.97030.02071.248-0.08870.1013-0.1153-0.4426-0.17530.07550.70760.1005-00.75190.08140.04110.5803-0.05890.680122.1863-31.6582-39.6608
20.8487-0.4731-0.86822.47280.70641.12250.04620.01410.0325-0.2188-0.18680.21870.0977-0.0681-00.43430.0322-0.03430.38720.03570.469915.7644-14.2558-29.221
31.51540.3191-0.192.99150.48231.36120.2078-0.01080.11130.3815-0.20240.1886-0.18020.1866-0.00010.4175-0.02160.06660.4882-0.00070.53278.17353.8895-15.6662
40.42480.67920.18590.79520.250.74310.1190.31120.1142-0.363-0.1169-0.0214-0.1701-0.26410.00010.5234-0.0272-0.00020.673-0.00210.502755.7859-39.821-11.6669
50.69810.26080.2411.0869-0.16230.00530.01260.0241-0.4481-0.0517-0.0079-0.3213-0.12070.05500.4368-0.05130.02410.57470.07940.576364.2926-49.7825-4.7083
61.6510.14530.22892.19710.57970.13610.0189-0.13470.1187-0.08570.0488-0.2154-0.14580.0452-00.5398-0.00150.01470.57280.04850.438459.6143-35.5362-2.4984
70.1330.2521-0.1920.24820.26810.40810.4455-0.4019-0.05910.8778-0.0641-0.3097-0.31690.18790.00010.8835-0.1729-0.02680.823-0.12730.775466.5974-18.727214.3535
81.68510.59760.31762.5523-0.36131.4483-0.0203-0.34460.24170.38350.025-0.1648-0.57570.1636-00.9273-0.0342-0.09940.6897-0.15270.582658.9417-13.632615.2606
9-0.0223-0.22370.50710.2339-0.08990.35050.34960.0495-0.2258-0.07680.6504-0.44320.6310.33760.00050.80170.0759-0.19751.09670.05731.114835.3768-22.0662-20.2289
10-0.0632-0.17130.3092-0.0054-0.22560.2646-0.10180.70860.1579-0.2387-0.53180.8451-0.4487-0.5493-0.00020.82340.1698-0.17091.14740.07420.93641.7458-28.406-9.4071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 80 )A8 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 287 )A81 - 287
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 380 )A288 - 380
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 41 )B7 - 41
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 109 )B42 - 109
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 193 )B110 - 193
7X-RAY DIFFRACTION7chain 'B' and (resid 194 through 228 )B194 - 228
8X-RAY DIFFRACTION8chain 'B' and (resid 229 through 380 )B229 - 380
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 11 )C1 - 11
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 11 )D1 - 11

+
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