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- PDB-5w45: Crystal structure of APOBEC3H -

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Basic information

Entry
Database: PDB / ID: 5w45
TitleCrystal structure of APOBEC3H
ComponentsAPOBEC3H
KeywordsDNA BINDING PROTEIN / Mutase
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / negative regulation by host of viral genome replication / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / negative regulation by host of viral genome replication / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / retrotransposon silencing / DNA demethylation / P-body / defense response to virus / hydrolase activity / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
APOBEC3H / APOBEC3 / 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
APOBEC3H / DNA dC->dU-editing enzyme APOBEC-3H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.486 Å
AuthorsIto, F. / Yang, H.J. / Xiao, X. / Li, S.X. / Wolfe, A. / Zirkle, B. / Arutiunian, V. / Chen, X.S.
CitationJournal: Sci Rep / Year: 2018
Title: Understanding the Structure, Multimerization, Subcellular Localization and mC Selectivity of a Genomic Mutator and Anti-HIV Factor APOBEC3H.
Authors: Ito, F. / Yang, H. / Xiao, X. / Li, S.X. / Wolfe, A. / Zirkle, B. / Arutiunian, V. / Chen, X.S.
History
DepositionJun 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: 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: APOBEC3H
B: APOBEC3H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5294
Polymers42,3992
Non-polymers1312
Water55831
1
A: APOBEC3H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,1991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APOBEC3H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,1991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.749, 65.006, 65.540
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 2 - 182 / Label seq-ID: 1 - 181

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein APOBEC3H /


Mass: 21199.336 Da / Num. of mol.: 2 / Fragment: residues 2-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3H / Production host: Escherichia coli (E. coli) / References: UniProt: B7TQM8, UniProt: Q6NTF7*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na thiocyanate 4% PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.486→46.749 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 1372 9.98 %
Rwork0.2112 12374 -
obs0.2136 13746 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204 Å2 / Biso mean: 65.406 Å2 / Biso min: 28 Å2
Refinement stepCycle: final / Resolution: 2.486→46.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 2 31 3009
Biso mean--45.68 52.72 -
Num. residues----362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023053
X-RAY DIFFRACTIONf_angle_d0.5514122
X-RAY DIFFRACTIONf_chiral_restr0.037430
X-RAY DIFFRACTIONf_plane_restr0.004536
X-RAY DIFFRACTIONf_dihedral_angle_d16.7511875
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1868X-RAY DIFFRACTION2.939TORSIONAL
12B1868X-RAY DIFFRACTION2.939TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.486-2.57490.35421120.32791107121987
2.5749-2.6780.31031410.28721197133898
2.678-2.79980.33121410.298512471388100
2.7998-2.94740.34031470.246912381385100
2.9474-3.1320.24491400.274812521392100
3.132-3.37380.26291350.236612551390100
3.3738-3.71320.25011380.212412401378100
3.7132-4.25020.22381440.188912691413100
4.2502-5.35360.18451400.172812651405100
5.3536-46.75720.17791340.169113041438100
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)
10.1118-0.07510.12180.5289-0.18840.89840.32110.05030.1242-0.0083-0.0773-0.04020.7322-0.02020.02780.4469-0.1037-0.070.35770.05140.4044238.2793-229.795626.8806
21.55410.8865-0.49172.6329-1.00881.80620.23-0.0410.04760.1489-0.18960.01430.10420.25940.00260.3249-0.0359-0.00920.31990.02960.3071248.0421-219.953626.2284
30.41790.6679-0.17270.8968-0.99171.3790.130.26120.25850.12190.08510.19690.0687-0.14480.00010.4675-0.03-0.07640.50070.05810.5808231.8041-223.550719.5272
40.23770.21630.00680.67470.14460.44760.2366-0.07620.0929-0.1053-0.0732-0.0807-0.5640.09280.00650.45720.08420.08120.35740.0730.4127238.2842-191.92695.8739
51.5818-0.71690.48272.9034-0.91161.60740.20660.0571-0.0408-0.1535-0.1792-0.0157-0.10970.28010.00850.32380.04180.01040.33790.04030.3076248.0627-201.77086.555
60.5065-0.77740.05770.8437-0.79951.34730.2937-0.1969-0.1359-0.0625-0.19930.26480.0481-0.3543-00.51590.04440.04980.51520.04680.6186231.8191-198.173613.2282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 36 )A2 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 148 )A37 - 148
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 182 )A149 - 182
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 36 )B2 - 36
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 148 )B37 - 148
6X-RAY DIFFRACTION6chain 'B' and (resid 149 through 182 )B149 - 182

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