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- PDB-8vud: Crystal structure of APOBEC3F-CD1 -

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Basic information

Entry
Database: PDB / ID: 8vud
TitleCrystal structure of APOBEC3F-CD1
ComponentsDNA dC->dU-editing enzyme APOBEC-3F
KeywordsRNA BINDING PROTEIN / APOBEC3F / HIV / Cytidine Deaminases
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / single-stranded DNA cytosine deaminase / base conversion or substitution editing / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / negative regulation of viral process / cytidine deaminase activity / transposable element silencing ...apolipoprotein B mRNA editing enzyme complex / single-stranded DNA cytosine deaminase / base conversion or substitution editing / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / negative regulation of viral process / cytidine deaminase activity / transposable element silencing / positive regulation of gene expression via chromosomal CpG island demethylation / negative regulation of viral genome replication / positive regulation of defense response to virus by host / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
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-3F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsYang, H.J. / Li, S.-X. / Pacheco, J. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150524 United States
CitationJournal: To Be Published
Title: Crystal Structure of APOBEC3F-CD1
Authors: Pacheco, J. / Yang, H.J. / Li, S.-X. / Chen, X.S.
History
DepositionJan 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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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-3F
B: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7566
Polymers46,4952
Non-polymers2624
Water30617
1
A: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3783
Polymers23,2471
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3783
Polymers23,2471
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.388, 124.388, 64.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3F / APOBEC3F-CD1 / Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F / A3F


Mass: 23247.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3F / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IUX4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris, pH 5.5, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 2.599→50 Å / Num. obs: 17567 / % possible obs: 99.9 % / Redundancy: 17.1 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.6914.30.88217510.8190.9490.2390.9151.099100
2.69-2.817.50.76217470.9080.9760.1870.7851.188100
2.8-2.9318.50.57117290.9510.9870.1370.5881.299.9
2.93-3.0818.60.4217390.9670.9920.1010.4321.24499.9
3.08-3.2818.80.3217550.9820.9950.0770.3291.15299.9
3.28-3.5318.50.22917470.990.9970.0560.2371.23699.8
3.53-3.8816.40.16317570.9920.9980.0440.1691.26899.8
3.88-4.45140.1117490.9960.9990.0320.1150.95299.9
4.45-5.615.90.09317720.9970.9990.0260.0970.92599.9
5.6-5018.10.07418210.99910.0180.0761.049100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→41.213 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1754 9.99 %
Rwork0.1783 --
obs0.1844 17563 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.599→41.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 4 17 3139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133216
X-RAY DIFFRACTIONf_angle_d1.3084364
X-RAY DIFFRACTIONf_dihedral_angle_d6.2431900
X-RAY DIFFRACTIONf_chiral_restr0.064436
X-RAY DIFFRACTIONf_plane_restr0.008568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.599-2.66920.33741320.25141195X-RAY DIFFRACTION99
2.6692-2.74780.29441340.21851210X-RAY DIFFRACTION100
2.7478-2.83640.2621340.20691212X-RAY DIFFRACTION100
2.8364-2.93780.26411350.19211198X-RAY DIFFRACTION100
2.9378-3.05540.30171330.19441207X-RAY DIFFRACTION100
3.0554-3.19440.22941360.18271213X-RAY DIFFRACTION100
3.1944-3.36270.27261280.18411223X-RAY DIFFRACTION100
3.3627-3.57330.26061330.17581212X-RAY DIFFRACTION100
3.5733-3.8490.21931380.17531196X-RAY DIFFRACTION100
3.849-4.2360.22841380.16541232X-RAY DIFFRACTION100
4.236-4.84810.20281390.13941207X-RAY DIFFRACTION100
4.8481-6.1050.23271340.17461234X-RAY DIFFRACTION100
6.105-41.2130.22691400.19481270X-RAY DIFFRACTION100
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)
10.6095-0.1093-0.35910.21230.16660.49260.00540.1137-0.1671-0.31790.0089-0.039-0.14840.2646-0.01520.189-0.01920.01970.35740.01580.3451-4.571654.7928-4.1034
22.1393-0.1658-0.6547-0.0070.2181.2832-0.03090.1137-0.503-0.0368-0.28180.12320.18350.2824-0.00230.3845-0.0403-0.01250.364-0.06540.5699-16.279743.1075-4.1675
31.4757-0.4963-0.36830.61021.12341.3133-0.13740.2198-0.2159-0.02580.05450.2976-0.22610.0744-0.00730.282-0.02920.01420.33660.01260.469-20.76151.3968-1.6645
41.3570.5199-0.2681.42320.44920.30130.0191-0.21380.00220.43380.04590.11230.14920.0972-0.00020.3478-0.0196-0.01170.38180.0310.3323-10.52857.0046.3377
50.23690.0393-0.47930.33310.68260.15110.3449-0.3545-0.0163-0.0164-0.44260.1318-0.3761-0.00640.00030.60110.0679-0.01250.6215-0.06010.4147-9.845557.093934.7049
6-0.05930.02130.3023-0.19210.2646-0.0810.02230.12460.0691-0.5181-0.68970.81850.1441-0.1796-0.06070.94580.0067-0.15540.6197-0.29730.733-16.671135.746427.2168
70.965-0.31630.58350.77350.40481.796-0.1141-0.1164-0.26310.1258-0.0538-0.05690.30090.1108-0.00020.55690.01750.05660.5335-0.11990.5576-4.160142.593734.7673
80.2756-0.174-0.33970.3446-0.02760.595-0.23110.5129-0.7139-0.42830.0382-0.43640.07270.03660.00020.73030.05470.03630.7627-0.18680.72944.843646.533625.9032
90.24440.0667-0.16160.1218-0.11750.3465-0.22-0.3984-0.0664-0.5634-0.50520.39910.776-0.4973-0.0150.68710.0081-0.1240.8694-0.09810.5612-16.229953.712925.557
100.45630.1860.32740.6745-0.52521.09550.46350.5824-0.0034-0.7244-0.38830.07550.1492-0.27120.00240.61120.0465-0.02450.5873-0.10150.2864-5.575959.06922.6808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 190 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 33 )
6X-RAY DIFFRACTION6chain 'B' and (resid 34 through 53 )
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 127 )
8X-RAY DIFFRACTION8chain 'B' and (resid 128 through 148 )
9X-RAY DIFFRACTION9chain 'B' and (resid 149 through 159 )
10X-RAY DIFFRACTION10chain 'B' and (resid 160 through 190 )

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