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- PDB-6p3x: Crystal Structure of Full Length APOBEC3G E/Q (pH 7.0) -

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Basic information

Entry
Database: PDB / ID: 6p3x
TitleCrystal Structure of Full Length APOBEC3G E/Q (pH 7.0)
ComponentsApolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
KeywordsRNA BINDING PROTEIN / APOBEC3G / HIV / Cytidine Deaminases
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
DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.402 Å
AuthorsYang, H.J. / Li, S.X. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087986 United States
CitationJournal: Nat Commun / Year: 2020
Title: Understanding the structural basis of HIV-1 restriction by the full length double-domain APOBEC3G.
Authors: Yang, H. / Ito, F. / Wolfe, A.D. / Li, S. / Mohammadzadeh, N. / Love, R.P. / Yan, M. / Zirkle, B. / Gaba, A. / Chelico, L. / Chen, X.S.
History
DepositionMay 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / struct_conn / struct_ncs_dom_lim
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
B: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5064
Polymers90,3752
Non-polymers1312
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-92 kcal/mol
Surface area35750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.495, 153.241, 67.494
Angle α, β, γ (deg.)90.000, 114.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 190 or resid 192...
21(chain B and (resid 4 through 190 or resid 192...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLY(chain A and (resid 4 through 190 or resid 192...AA4 - 19011 - 193
12LEULEULEULEU(chain A and (resid 4 through 190 or resid 192...AA192 - 193195 - 196
13HISHISHISHIS(chain A and (resid 4 through 190 or resid 192...AA195198
21GLNGLNGLYGLY(chain B and (resid 4 through 190 or resid 192...BB4 - 19011 - 193
22LEULEULEULEU(chain B and (resid 4 through 190 or resid 192...BB192 - 193195 - 196
23GLNGLNZNZN(chain B and (resid 4 through 190 or resid 192...BB - D4 - 70111

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Components

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


Mass: 45187.430 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM HEPES, pH 7 1.6 M ammonium sulfate 10 mM MgCl2

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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: Jun 5, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 47476 / % possible obs: 98.3 % / Redundancy: 6.7 % / Net I/σ(I): 18.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.9 % / Num. unique obs: 4210 / % possible all: 87.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.402→47.835 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 1993 4.21 %
Rwork0.1886 45326 -
obs0.1906 47319 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.31 Å2 / Biso mean: 53.1216 Å2 / Biso min: 16.98 Å2
Refinement stepCycle: final / Resolution: 2.402→47.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 2 196 6240
Biso mean--40.4 47.99 -
Num. residues----724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2138X-RAY DIFFRACTION1.53TORSIONAL
12B2138X-RAY DIFFRACTION1.53TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4021-2.46210.24711240.22292706283082
2.4621-2.52870.29781320.22563016314892
2.5287-2.60310.29241450.23643287343298
2.6031-2.68710.27631420.22483299344199
2.6871-2.78310.28161410.226732583399100
2.7831-2.89460.29431450.217933033448100
2.8946-3.02630.23251460.213332973443100
3.0263-3.18580.26521470.206733023449100
3.1858-3.38540.25631490.191833193468100
3.3854-3.64670.24531430.183833023445100
3.6467-4.01350.21771440.166933113455100
4.0135-4.59380.191450.150833053450100
4.5938-5.78610.20991460.166633273473100
5.7861-47.84460.22861440.19373294343898
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)
11.8920.73960.11534.8536-0.18421.11740.00480.0410.3298-0.46920.01780.2469-0.2062-0.0546-0.00840.29330.02920.01070.2698-0.02010.2254.788417.7484-3.0627
26.5802-0.10580.14653.4454-0.95911.8815-0.1228-0.12060.61710.060.10070.1139-0.1283-0.09730.0260.25110.0254-0.04580.3631-0.02180.499633.31515.64236.7871
31.28130.4626-0.17964.9533-0.67971.7678-0.05280.0696-0.2288-0.42460.03340.32920.3302-0.00760.03260.25110.0364-0.01740.2541-0.01730.2661-4.8249-17.41533.0395
42.87740.9815-1.99143.71290.30355.9903-0.20870.0284-0.1445-0.03620.1236-0.11540.61040.18980.03750.49760.03320.0520.3773-0.01350.2402-7.8637-5.322533.0634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 206 )A4 - 206
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 383 )A207 - 383
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 206 )B4 - 206
4X-RAY DIFFRACTION4chain 'B' and (resid 207 through 383 )B207 - 383

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