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

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Basic information

Entry
Database: PDB / ID: 5cqd
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 / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / P-body ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / 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
DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsShi, K. / Kurahashi, K. / Aihara, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095558 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109770 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI064046 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 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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


Theoretical massNumber of molelcules
Total (without water)44,5499
Polymers43,9582
Non-polymers5917
Water1,35175
1
A: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4136
Polymers21,9791
Non-polymers4345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1363
Polymers21,9791
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.440, 50.840, 70.150
Angle α, β, γ (deg.)90.00, 100.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21978.963 Da / Num. of mol.: 2 / Fragment: UNP Residues 187-378 / Mutation: F200S, W228S, L230K, Y250S, F308K
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→52.8 Å / Num. obs: 18464 / % possible obs: 86 % / Redundancy: 2.4 % / Rmerge F obs: 0.076 / Net I/σ(I): 12.4
Reflection shellResolution: 2.08→2.16 Å / Rmerge(I) obs: 0.446

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Processing

Software
NameVersionClassification
PHENIX(dev_2166: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V4K

3v4k


Resolution: 2.08→46.14 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 971 5 %Random selection
Rwork0.1877 ---
obs0.1897 18464 90.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 32 75 3170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053192
X-RAY DIFFRACTIONf_angle_d0.5664313
X-RAY DIFFRACTIONf_dihedral_angle_d17.6551881
X-RAY DIFFRACTIONf_chiral_restr0.043444
X-RAY DIFFRACTIONf_plane_restr0.003561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0802-2.13230.3421800.33071453X-RAY DIFFRACTION49
2.1323-2.18990.37231210.30322221X-RAY DIFFRACTION75
2.1899-2.25430.39791190.31412349X-RAY DIFFRACTION80
2.2543-2.32710.3191420.28992642X-RAY DIFFRACTION89
2.3271-2.41030.29231460.25972814X-RAY DIFFRACTION95
2.4103-2.50680.31141550.2452864X-RAY DIFFRACTION99
2.5068-2.62080.27181530.20932949X-RAY DIFFRACTION99
2.6208-2.7590.26311530.21472891X-RAY DIFFRACTION98
2.759-2.93180.23261540.20632910X-RAY DIFFRACTION98
2.9318-3.15820.2051540.19732934X-RAY DIFFRACTION99
3.1582-3.47590.24581500.18042857X-RAY DIFFRACTION97
3.4759-3.97860.19331500.16592822X-RAY DIFFRACTION95
3.9786-5.01170.1661460.14432816X-RAY DIFFRACTION95
5.0117-46.15150.21971450.17332884X-RAY DIFFRACTION97
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)
10.23350.19280.11630.160.09610.0570.163-0.1017-0.24620.0205-0.1277-0.098-0.12820.1971-00.49640.02750.00340.4083-0.03640.529879.93662.6578-1.3874
20.58190.3353-0.32970.8975-0.22720.44630.0514-0.10310.0048-0.0547-0.0270.0075-0.0658-0.006600.4231-0.0076-0.00930.45560.0110.425571.350211.82912.8985
30.0395-0.0099-0.04240.0206-0.00290.05420.07350.22540.1308-0.071-0.1593-0.1559-0.50190.194200.4954-0.03010.02720.5082-0.00540.485161.926520.8272-32.7342
40.2051-0.05720.12980.2261-0.36740.61880.0717-0.04860.0329-0.11510.05540.0378-0.032-0.11100.4157-0.0191-0.0190.43080.01430.443845.080312.637-34.4006
50.1626-0.36560.2890.851-0.67840.54670.01170.03060.0624-0.0719-0.0109-0.10120.26220.08740.00090.424-0.01730.00030.4018-0.010.414559.03489.7334-27.5433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 186 through 214 )
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 378 )
3X-RAY DIFFRACTION3chain 'C' and (resid 188 through 214 )
4X-RAY DIFFRACTION4chain 'C' and (resid 215 through 309 )
5X-RAY DIFFRACTION5chain 'C' and (resid 310 through 379 )

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