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- PDB-6p3y: Crystal Structure of Full Length APOBEC3G E/Q (pH 7.4) -

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Basic information

Entry
Database: PDB / ID: 6p3y
TitleCrystal Structure of Full Length APOBEC3G E/Q (pH 7.4)
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 / deoxycytidine deaminase activity / cytidine deaminase activity / retrotransposon silencing / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / zinc ion binding / nucleus
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-3G
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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 1.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / 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

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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
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-93 kcal/mol
Surface area36180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.695, 153.849, 67.728
Angle α, β, γ (deg.)90.000, 116.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 14 or resid 16...
21(chain B and (resid 4 through 14 or resid 16...

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
11GLNGLNPROPRO(chain A and (resid 4 through 14 or resid 16...AA4 - 1411 - 21
12THRTHRTHRTHR(chain A and (resid 4 through 14 or resid 16...AA16 - 4123 - 48
13ASPASPSERSER(chain A and (resid 4 through 14 or resid 16...AA43 - 1950 - 26
14HISHISLEULEU(chain A and (resid 4 through 14 or resid 16...AA195 - 242198 - 245
15ASNASNZNZN(chain A and (resid 4 through 14 or resid 16...AA - C244 - 701247
21GLNGLNPROPRO(chain B and (resid 4 through 14 or resid 16...BB4 - 1411 - 21
22THRTHRTHRTHR(chain B and (resid 4 through 14 or resid 16...BB16 - 4123 - 48
23ASPASPLEULEU(chain B and (resid 4 through 14 or resid 16...BB43 - 19350 - 196
24HISHISLEULEU(chain B and (resid 4 through 14 or resid 16...BB195 - 242198 - 245
25ASNASNZNZN(chain B and (resid 4 through 14 or resid 16...BB - D244 - 701247

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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: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 50 mM Tris, pH 7.4 1.9 M ammonium sulfate 25 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: 2.58→50 Å / Num. obs: 38586 / % possible obs: 98.1 % / Redundancy: 6.6 % / Net I/σ(I): 15.4
Reflection shellResolution: 2.58→2.67 Å / Num. unique obs: 3355

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→39.169 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 2015 5.23 %
Rwork0.1956 36513 -
obs0.1978 38528 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.48 Å2 / Biso mean: 55.511 Å2 / Biso min: 16.31 Å2
Refinement stepCycle: final / Resolution: 2.57→39.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 2 113 6157
Biso mean--42.83 45.95 -
Num. residues----724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2138X-RAY DIFFRACTION1.257TORSIONAL
12B2138X-RAY DIFFRACTION1.257TORSIONAL
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 (%)
2.5699-2.63410.36441220.27872110223279
2.6341-2.70530.38281310.26942442257391
2.7053-2.78490.31541290.25192558268797
2.7849-2.87480.26141540.24842643279799
2.8748-2.97750.28091430.231727092852100
2.9775-3.09670.28321530.23526492802100
3.0967-3.23750.27451470.223126742821100
3.2375-3.40810.2591590.194826592818100
3.4081-3.62150.19631460.183626342780100
3.6215-3.90090.21921490.174526752824100
3.9009-4.29310.18831450.163526782823100
4.2931-4.91320.20131440.147226802824100
4.9132-6.18620.22811610.195926802841100
6.1862-39.17320.20911320.191527222854100
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)
11.97460.2468-1.88473.73080.15584.9938-0.06560.0102-0.00280.31590.03080.15460.20590.1275-0.00710.58290.01070.13640.3887-0.03610.31-8.7619-5.290732.8376
22.53861.5983-0.53167.698-1.18261.4669-0.0430.04930.4709-0.92330.05410.71-0.2042-0.06450.07180.36970.0534-0.04630.2614-0.0220.27383.944820.6131-4.0569
35.3339-0.49011.42082.5951-0.00480.46950.084-0.143-0.16450.0544-0.0486-0.59270.09550.16280.0110.29110.03410.04350.40060.01790.482320.26223.10256.3881
45.7625-0.0986-0.10572.97990.12091.2576-0.0488-0.050.2189-0.01170.0391-0.4571-0.0175-0.05710.00040.25630.0256-0.00250.38490.00020.667735.03275.80976.1492
51.47041.1565-0.57437.3158-0.82392.2591-0.09260.0218-0.1769-0.89150.05320.52490.4201-0.01460.04370.25270.04-0.05780.2679-0.03050.2856-4.8091-17.4932.9086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 207 through 383 )B207 - 383
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 177 )A4 - 177
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 244 )A178 - 244
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 383 )A245 - 383
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 206 )B4 - 206

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