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- PDB-3ir2: Crystal structure of the APOBEC3G catalytic domain -

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Basic information

Entry
Database: PDB / ID: 3ir2
TitleCrystal structure of the APOBEC3G catalytic domain
ComponentsDNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE / APOBEC3G / ANTIVIRAL DEFENSE / HOST-VIRUS INTERACTION / METAL-BINDING / Nucleus
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of viral process ...apolipoprotein B mRNA editing enzyme complex / dCTP deaminase activity / cytidine deamination / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of viral process / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / negative regulation of viral genome replication / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of defense response to virus by host / Vif-mediated degradation of APOBEC3G / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
APOBEC-like C-terminal domain / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsShandilya, S.M.D. / Schiffer, C.A.
CitationJournal: Structure / Year: 2010
Title: Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces.
Authors: Shandilya, S.M. / Nalam, M.N. / Nalivaika, E.A. / Gross, P.J. / Valesano, J.C. / Shindo, K. / Li, M. / Munson, M. / Royer, W.E. / Harjes, E. / Kono, T. / Matsuo, H. / Harris, R.S. / ...Authors: Shandilya, S.M. / Nalam, M.N. / Nalivaika, E.A. / Gross, P.J. / Valesano, J.C. / Shindo, K. / Li, M. / Munson, M. / Royer, W.E. / Harjes, E. / Kono, T. / Matsuo, H. / Harris, R.S. / Somasundaran, M. / Schiffer, C.A.
History
DepositionAug 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3G
B: DNA dC->dU-editing enzyme APOBEC-3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,55710
Polymers48,1762
Non-polymers3818
Water6,792377
1
A: DNA dC->dU-editing enzyme APOBEC-3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2795
Polymers24,0881
Non-polymers1914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA dC->dU-editing enzyme APOBEC-3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2795
Polymers24,0881
Non-polymers1914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.338, 72.532, 97.433
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3G / APOBEC-related cytidine deaminase / ARCD / APOBEC-related protein / ARP-9 / CEM-15 / CEM15


Mass: 24088.059 Da / Num. of mol.: 2 / Fragment: C-Terminal Domain / Mutation: L234K, C243A, F310K, C321A, C356A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G, MDS019 / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus DE3-(RIL)
References: UniProt: Q9HC16, 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 10% PEG 4000, 0.1M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2009 / Details: Bent conical Si-mirror (Rh coated)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2.25→58.22 Å / Num. all: 23001 / Num. obs: 23001 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.365 / Num. unique all: 2260 / Rsym value: 0.365 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0093refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Highly truncated model based on PDB Entry 3E1U

3e1u


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.639 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20823 1171 5.1 %RANDOM
Rwork0.16569 ---
all0.16783 23001 --
obs0.16783 21796 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.463 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---1.47 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 8 377 3371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213079
X-RAY DIFFRACTIONr_bond_other_d0.0060.022036
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9034189
X-RAY DIFFRACTIONr_angle_other_deg0.86734898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79123.354161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00915451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4411520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
X-RAY DIFFRACTIONr_mcbond_it0.5351.51869
X-RAY DIFFRACTIONr_mcbond_other0.1191.5752
X-RAY DIFFRACTIONr_mcangle_it1.01122981
X-RAY DIFFRACTIONr_scbond_it1.49831210
X-RAY DIFFRACTIONr_scangle_it2.3154.51208
LS refinement shellResolution: 2.25→2.306 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 85 -
Rwork0.194 1519 -
obs--94.35 %
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)
115.4668-0.0319-1.06734.29982.48892.2619-0.0581-0.54970.9250.3220.4027-0.3127-0.20370.202-0.34460.2144-0.0307-0.00010.2749-0.09320.255519.96580.40339.3616
21.5528-0.386-0.24581.35650.8240.82120.0279-0.10370.05540.0567-0.04580.14280.01550.03590.0180.1036-0.00260.00260.1238-0.00420.10427.2531-2.89844.7902
35.9161-1.2812-3.05590.7439-0.12443.1187-0.0617-0.2289-0.1064-0.02860.0168-0.04530.030.41750.04490.1622-0.0476-0.00740.1688-0.00670.179625.2022-2.3895-7.1151
411.2005-4.423-1.55283.52633.67133.2047-0.03070.1559-0.7269-0.1510.09010.08890.33830.295-0.05930.36530.02640.07540.28370.04510.301133.8154-12.4225-15.0793
58.7727-0.4831-1.765526.88164.151615.0574-0.154-0.15090.32670.47410.36680.5517-0.3485-0.1218-0.21270.0925-0.0030.0130.2231-0.01880.171533.0378-3.0006-6.3647
62.4037-4.18221.50147.7963-1.32211.81750.00140.04920.1380.05110.0233-0.2968-0.07990.0448-0.02470.1349-0.038-0.00720.1415-0.01240.176820.06435.9842-1.3447
70.194-1.014-0.05054.2606-2.95064.19930.06110.0412-0.1788-0.12490.05240.75620.1324-0.2449-0.11350.20350.01620.02210.2104-0.01530.27479.293519.9412-4.6246
83.90820.4839-0.50240.4066-0.01642.8436-0.05970.14160.0798-0.2631-0.0299-0.0436-0.05880.02820.08960.1521-0.01910.01740.13930.00960.161718.08658.0396-9.4146
94.5656-0.45156.256618.16235.21284.77450.01950.03490.37810.1438-0.13540.19770.01770.13650.11590.1515-0.02480.07860.1929-0.03420.191129.35526.7616-12.3746
104.45721.7443-2.90021.0984-1.91534.29170.020.05040.0505-0.1678-0.0571-0.02210.21470.12440.03710.16060.00290.02660.1890.01090.14430.6742-2.6899-17.4746
111.64650.05171.65081.25890.0462.728-0.00830.27490.0574-0.0831-0.0156-0.11880.03720.02610.0240.1442-0.00190.02110.12450.00540.154511.53340.3135-8.1128
127.57572.53-6.10579.11684.29297.37370.16580.43670.4963-0.215-0.07660.4555-0.4533-0.315-0.08920.2339-0.0269-0.04630.24340.06720.11313.79314.2063-18.171
1315.451-2.79360.35370.3163-1.7789.9084-0.12260.4465-0.0365-0.1369-0.06530.07710.0618-0.1750.18780.24380.0007-0.01560.19170.03160.144221.94411.4649-21.8692
142.24491.0981-0.45340.9179-0.39781.1050.01580.27080.0087-0.15190.0008-0.00840.0217-0.0984-0.01660.12630.03750.00880.14250.00150.102715.4006-4.0518-9.9806
156.041-2.0365-2.42351.96451.04643.90370.03080.1335-0.0276-0.06610.0225-0.0014-0.0384-0.0061-0.05330.0967-0.0305-0.00660.1019-0.00240.04856.499-2.5561-16.1794
162.1722-0.33330.33121.5938-0.07870.08220.0183-0.07880.06110.06720.0012-0.21230.0820.1236-0.01950.11040.0254-0.00780.147-0.01530.127220.2053-9.27611.8181
1714.02324.41873.04641.59290.75060.66670.0107-0.36340.44990.3765-0.20130.2407-0.09110.01490.19050.3559-0.0162-0.01420.3095-0.01160.211322.5931-10.000912.2067
183.49751.76744.63574.5591-0.9068.5202-0.102-0.564-0.05520.4107-0.02360.19490.1139-0.33820.12560.19540.05380.04550.19570.02770.15748.9047-13.80545.6848
193.97212.11981.73182.996-0.70498.0093-0.0503-0.0626-0.18190.16890.1250.3296-0.0032-0.3745-0.07460.10960.0148-0.00580.09830.00790.1485.7769-13.2515-6.2393
2013.1944-6.5550.207722.6487-1.303616.21770.19080.4266-0.7222-1.18410.1670.760.5598-0.0894-0.35770.2048-0.0353-0.10340.23840.01190.22844.2326-12.1087-15.7162
219.4713-2.3665-0.05530.85941.20463.0851-0.4954-0.4539-0.88010.30820.24180.08920.1938-0.03530.25350.2647-0.0457-0.00770.26320.0090.289213.9966-37.29397.8016
224.045-2.39131.8224.1302-0.27060.4639-0.0453-0.18630.1814-0.00860.0266-0.2869-0.0508-0.1340.01870.14560.01720.02520.16440.00010.167520.7536-33.69814.2241
235.0937-1.6721.1583.54130.7629-0.2031-0.08250.09170.52390.2113-0.0586-0.3858-0.00290.04440.14110.1537-0.00070.00890.24210.04080.199532.0125-30.41752.6916
246.13320.22197.64045.11043.94298.80970.2397-0.1395-0.4780.27470.20810.05950.4834-0.0268-0.44780.2069-0.02450.0180.1980.02950.146426.0411-40.84981.5206
256.37-1.7634.36261.5286-0.4126.3441-0.21160.0340.19450.1085-0.08830.1083-0.0891-0.12960.29980.0451-0.04370.01140.0803-0.00230.10628.9323-35.2688-8.6575
267.30790.83933.74144.16971.27237.08720.10490.32550.6084-0.4468-0.16390.2684-0.5201-0.45440.05890.20250.0424-0.01950.28080.04280.2452-0.1683-26.2457-18.8232
273.78950.40040.696623.6714-9.35845.44730.0677-0.37560.05350.3535-0.3595-0.3229-0.1333-0.1880.29190.08510.0294-0.00370.287-0.00730.12760.537-34.1404-9.0778
280.28680.3370.46072.9395-0.47381.12750.0280.0742-0.0475-0.0031-0.0145-0.17050.10970.0897-0.01350.1034-0.02540.00240.0931-0.00090.103220.2289-50.3249-5.1106
291.7551-1.43861.35710.8601-0.8241.3710.0534-0.0225-0.3344-0.10640.05090.19230.0345-0.2181-0.10440.1533-0.0266-0.03190.2148-0.01910.18736.4728-44.2138-14.7386
301.71912.82043.68594.07934.07068.9779-0.02250.00050.2283-0.1362-0.11630.3561-0.0026-0.01740.13880.15830.02590.02960.2123-0.01380.17796.669-34.0172-16.0616
312.3273-1.4055-0.89154.58534.003711.1106-0.02410.1134-0.1673-0.00610.00530.0440.0049-0.03020.01880.0897-0.02610.01330.07820.00410.114324.9636-38.9045-9.6628
329.3471-1.35545.36088.2242-5.345610.75810.09570.3137-0.5077-0.2065-0.2188-0.17180.34610.11550.12310.096-0.01280.01430.1166-0.0440.073320.4741-42.7966-18.3451
331.85470.13850.92930.53880.38871.115-0.01470.2261-0.0472-0.1071-0.040.0203-0.0397-0.02130.05470.1250.00780.00780.1426-0.00680.115117.687-36.0288-14.8954
348.5417-3.49435.30393.8717-5.52337.75770.07470.1959-0.3504-0.0620.18760.08780.21070.0594-0.26230.13620.01960.00540.1797-0.04760.122933.5082-38.2498-15.4841
350.8695-0.1356-1.00320.23820.33422.61540.03420.1348-0.0255-0.0814-0.03650.0367-0.0554-0.10180.00230.0970.0143-0.00040.1320.00890.082321.188-30.3117-14.2312
368.02860.4348-2.062.55750.51136.3321-0.02870.4995-0.13750.00950.00960.3777-0.1648-0.41090.01910.09130.03620.0070.107-0.00210.14612.3559-27.33740.9079
374.7982.6541-2.70193.6126-1.12521.67390.2723-0.40390.15640.3144-0.20560.2491-0.11830.0361-0.06670.20850.03480.01210.23810.00850.163412.9305-28.33956.8462
3814.4779-0.5744-5.43470.90493.96098.73350.1636-0.24060.4480.05750.073-0.1512-0.11480.0136-0.23660.17710.0291-0.03590.0962-0.02310.199425.4458-21.4931-0.4147
398.99262.81630.81692.79012.71646.2596-0.0702-0.18880.17810.03950.123-0.0794-0.16490.3175-0.05280.11750.01-0.01410.12720.0190.145828.7621-24.1818-8.9555
407.36942.94493.419213.9155-4.02872.2891-0.28810.95580.3351-0.32410.1613-0.1459-0.03090.20550.12680.24570.0093-0.01010.297-0.01110.134129.8871-26.376-17.9444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A196 - 201
2X-RAY DIFFRACTION2A202 - 216
3X-RAY DIFFRACTION3A217 - 228
4X-RAY DIFFRACTION4A229 - 233
5X-RAY DIFFRACTION5A234 - 238
6X-RAY DIFFRACTION6A239 - 245
7X-RAY DIFFRACTION7A246 - 255
8X-RAY DIFFRACTION8A256 - 265
9X-RAY DIFFRACTION9A266 - 270
10X-RAY DIFFRACTION10A271 - 280
11X-RAY DIFFRACTION11A281 - 291
12X-RAY DIFFRACTION12A292 - 297
13X-RAY DIFFRACTION13A298 - 303
14X-RAY DIFFRACTION14A304 - 315
15X-RAY DIFFRACTION15A316 - 334
16X-RAY DIFFRACTION16A335 - 353
17X-RAY DIFFRACTION17A354 - 359
18X-RAY DIFFRACTION18A360 - 367
19X-RAY DIFFRACTION19A368 - 375
20X-RAY DIFFRACTION20A376 - 381
21X-RAY DIFFRACTION21B196 - 201
22X-RAY DIFFRACTION22B202 - 207
23X-RAY DIFFRACTION23B208 - 213
24X-RAY DIFFRACTION24B214 - 218
25X-RAY DIFFRACTION25B219 - 227
26X-RAY DIFFRACTION26B228 - 232
27X-RAY DIFFRACTION27B233 - 238
28X-RAY DIFFRACTION28B239 - 261
29X-RAY DIFFRACTION29B262 - 273
30X-RAY DIFFRACTION30B274 - 282
31X-RAY DIFFRACTION31B283 - 290
32X-RAY DIFFRACTION32B291 - 297
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