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- PDB-5cqh: Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B -

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Basic information

Entry
Database: PDB / ID: 5cqh
TitleCrystal Structure of the Cancer Genomic DNA Mutator APOBEC3B
ComponentsDNA dC-dU-editing enzyme APOBEC-3B
KeywordsHYDROLASE / APOBEC / deaminase
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 / 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 ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / 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 / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.73 Å
AuthorsShi, K. / Kurahashi, K. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
Authors: Shi, K. / Carpenter, M.A. / Kurahashi, K. / Harris, R.S. / Aihara, H.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6358
Polymers21,9791
Non-polymers6567
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.843, 52.448, 68.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA dC-dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3


Mass: 21978.963 Da / Num. of mol.: 1 / Fragment: UNP Residues 187-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UH17, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines

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Non-polymers , 5 types, 192 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DC / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Deoxycytidine monophosphate


Type: DNA linking / Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P / Comment: dCMP*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, MES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.73→40.7 Å / Num. obs: 19558 / % possible obs: 100 % / Redundancy: 4.7 % / Net I/σ(I): 17.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2067: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.73→40.7 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 998 5.11 %Random selection
Rwork0.1523 ---
obs0.1541 19544 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 38 185 1739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181614
X-RAY DIFFRACTIONf_angle_d1.6522189
X-RAY DIFFRACTIONf_dihedral_angle_d17.201948
X-RAY DIFFRACTIONf_chiral_restr0.1225
X-RAY DIFFRACTIONf_plane_restr0.01285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7301-1.82130.2941370.23062615X-RAY DIFFRACTION100
1.8213-1.93540.22681480.17812581X-RAY DIFFRACTION100
1.9354-2.08480.19981210.15842655X-RAY DIFFRACTION100
2.0848-2.29460.19011600.14442603X-RAY DIFFRACTION100
2.2946-2.62660.18151660.1442625X-RAY DIFFRACTION100
2.6266-3.3090.17771260.14942686X-RAY DIFFRACTION100
3.309-40.73830.16141400.14072781X-RAY DIFFRACTION99
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)
16.922.1456-1.42885.8884-2.52376.0428-0.0060.42560.0791-0.31170.1543-0.25040.10610.0803-0.07530.10330.0250.00460.1739-0.0270.0932-0.6908-11.9846-4.1927
22.11780.2958-0.082.519-0.19071.94610.0602-0.0475-0.0769-0.0283-0.0649-0.0299-0.02070.0372-0.01690.09510.0161-0.00230.1157-0.00670.0593-5.6082-10.60884.6285
35.426-4.80212.37816.2463-1.59432.55190.00150.2150.3324-0.3552-0.11960.2546-0.2948-0.24680.05890.21420.0378-0.01480.1950.03130.1854-10.99681.9111-2.8619
41.01960.16340.08121.33060.18881.90460.015-0.03690.10920.0961-0.02360.0022-0.1431-0.02360.01830.08390.0050.00140.11420.00060.105-8.5535-4.92829.8818
52.02611.2827-0.85121.9023-1.13354.6096-0.04290.1694-0.2541-0.12970.035-0.03940.3527-0.1637-0.00530.06270.0067-0.04870.1191-0.0140.1111-12.1216-19.18682.4583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 189 through 202 )
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 224 )
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 348 )
5X-RAY DIFFRACTION5chain 'A' and (resid 349 through 379 )

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