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- PDB-6nfm: Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with... -

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Basic information

Entry
Database: PDB / ID: 6nfm
TitleCrystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G
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 / 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 / cytidine deaminase activity / transposable element silencing / P-body ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / 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 / cytidine deaminase activity / 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: 2.53 Å
AuthorsShi, K. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Faseb Bioadv / Year: 2020
Title: Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B
Authors: Shi, K. / Demir, O. / Carpenter, M.A. / Banerjee, S. / Harki, D.A. / Amaro, R.E. / Harris, R.S. / Aihara, H.
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,8802
Polymers22,8451
Non-polymers351
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.314, 50.314, 149.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 22844.803 Da / Num. of mol.: 1
Mutation: F200S, W228S, L230K, Y250S, F308K, Y315D, D316Q, P317G, L318R, Y319C, K320Q
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, single-stranded DNA cytosine deaminase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: LiCl, HEPES,PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.53→41.8 Å / Num. obs: 6968 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.07 / Rrim(I) all: 0.19 / Rsym value: 0.18 / Net I/σ(I): 10.9
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 674 / CC1/2: 0.5 / Rpim(I) all: 0.7 / Rrim(I) all: 1.9 / Rsym value: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_3357: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQD

5cqd


Resolution: 2.53→41.766 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.29
RfactorNum. reflection% reflection
Rfree0.2757 325 4.67 %
Rwork0.2181 --
obs0.2207 6965 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.53→41.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 1 22 1533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031548
X-RAY DIFFRACTIONf_angle_d0.5312097
X-RAY DIFFRACTIONf_dihedral_angle_d19.966920
X-RAY DIFFRACTIONf_chiral_restr0.04217
X-RAY DIFFRACTIONf_plane_restr0.003276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-3.18740.34441740.27353205X-RAY DIFFRACTION100
3.1874-41.77190.2511510.20173435X-RAY DIFFRACTION100

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