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

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Basic information

Entry
Database: PDB / ID: 5sxh
TitleCrystal Structure of the Cancer Genomic DNA Mutator APOBEC3B
ComponentsDNA dC->dU-editing enzyme APOBEC-3B
KeywordsHYDROLASE / 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
DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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)GM095558 and GM109770 United States
CitationJournal: Sci Rep / Year: 2017
Title: Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Authors: Shi, K. / Demir, O. / Carpenter, M.A. / Wagner, J. / Kurahashi, K. / Harris, R.S. / Amaro, R.E. / Aihara, H.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_detector ...chem_comp / diffrn_detector / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _diffrn_detector.detector ..._chem_comp.name / _diffrn_detector.detector / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.3Oct 4, 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
Revision 2.0Jan 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity_src_gen / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / struct_site / struct_site_gen / symmetry
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _cell.volume / _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine_hist.d_res_low / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _symmetry.space_group_name_Hall

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


Theoretical massNumber of molelcules
Total (without water)43,9607
Polymers43,6432
Non-polymers3175
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.390, 50.990, 77.410
Angle α, β, γ (deg.)90.000, 101.960, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 190 through 224 or resid 233...
d_2ens_1(chain "B" and ((resid 190 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGASPASPAA190 - 2245 - 39
d_12GLNGLNTHRTHRAA233 - 30148 - 108
d_13VALVALASPASPAA303 - 314110 - 121
d_14ASPASPGLNGLNAA316 - 378123 - 185
d_15ZNZNZNZNAC401
d_16EDOEDOEDOEDOAD402
d_21ARGARGTHRTHRBB190 - 3015 - 108
d_22VALVALASPASPBB303 - 314110 - 121
d_23ASPASPGLNGLNBB316 - 378123 - 185
d_24ZNZNZNZNBF401
d_25EDOEDOEDOEDOBG402

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Components

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


Mass: 21821.688 Da / Num. of mol.: 2 / Mutation: F200S, W228S, L230K, Y250S, F308K, Delta 242-249
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: PEG3350

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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: Oct 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→75.55 Å / Num. obs: 32228 / % possible obs: 98.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.8
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1 / CC1/2: 0.376 / % possible all: 99.1

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Processing

Software
NameVersionClassification
phenix.refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQK

5cqk


Resolution: 1.78→41.57 Å / SU ML: 0.2408 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2157 1611 5 %
Rwork0.1854 30602 -
obs0.1869 32213 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.28 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 14 207 3108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393002
X-RAY DIFFRACTIONf_angle_d0.76244070
X-RAY DIFFRACTIONf_chiral_restr0.0497414
X-RAY DIFFRACTIONf_plane_restr0.0069532
X-RAY DIFFRACTIONf_dihedral_angle_d12.22071095
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.68676374973 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.35871430.31882524X-RAY DIFFRACTION98.38
1.83-1.890.2991530.29972470X-RAY DIFFRACTION98.39
1.89-1.960.31961190.27972528X-RAY DIFFRACTION98.18
1.96-2.040.2811480.24092579X-RAY DIFFRACTION99.53
2.04-2.130.25381170.21072550X-RAY DIFFRACTION99
2.13-2.240.25931280.20542559X-RAY DIFFRACTION98.93
2.24-2.380.24421260.19462521X-RAY DIFFRACTION98.04
2.38-2.570.23161320.18082563X-RAY DIFFRACTION99.12
2.57-2.830.19451440.18112550X-RAY DIFFRACTION99.04
2.83-3.230.21641330.17452549X-RAY DIFFRACTION98.06
3.23-4.070.19091240.1522583X-RAY DIFFRACTION98.9
4.07-41.570.15831440.15612626X-RAY DIFFRACTION98.44
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)
13.4920689291-0.322403300267-0.245477773022.065338390760.4482850885721.22775713940.03051592128720.21841090148-0.0459703837518-0.0379281009228-0.0123720518409-0.07936220001780.04484153986230.045153470905-0.01595284007620.190334748881-0.00570527000781-0.01791443166940.197500821855-0.01163484861710.1884687957426.90858355231.889860474860.116809880558
23.149759933740.915068362702-1.847797820031.83442058041-1.60319443463.01512360281-0.00456020079767-0.09791119016360.0184077606825-0.0196758844121-0.023058208851-0.1984876250030.05267599469310.1154809271420.03662836999270.192663376022-0.0101205114099-0.0401230312360.200319621418-0.01157286748930.24496783979614.66506319778.278407378895.58994652194
32.30852061959-0.5422600571760.3639321968941.813978630550.8246039637622.32342974615-0.0324194139526-0.02214190293650.029954733232-0.0803405182751-0.06548419445460.0930950811919-0.132763768978-0.04268240224250.1252012181430.1646126001630.00316685744622-0.007801867758720.1567908321490.01755543083890.1943136505340.41921697433911.43154804485.74841359819
43.13469958162-0.159684264638-0.54947531733.32644596064-0.7152534874922.79601068759-0.0765138155852-0.062509256263-0.181354186014-0.0806446538703-0.0863358852681-0.118578969910.187630332085-0.07875238085950.2253133146250.170848774473-0.0101299624107-0.03159095984810.2090734633550.006621912527630.2172314529135.237002348-3.6077177648936.3787524438
54.15930978071-2.35612714203-0.6172806663766.03152584367-0.9014248416220.677888379214-0.111128574422-0.288791891518-0.1140189462180.2263522452570.08383325175280.244707063823-0.0548618182739-0.09434630814060.04526471917060.2024361769530.0144274846630.005696925277830.273315399570.01129202108310.24307429845522.7473616925-4.4636062217641.3122002359
65.0760732478-1.65501580966-1.828599061572.231903703261.175143100022.768430145630.00933906221643-0.284374793290.0659950295821-0.00837020020309-0.03045007447840.1724657871970.033027022136-0.251399830840.008584124990270.240888220560.00511215872701-0.03173950062910.301925198760.02088604531070.23529131294519.48526816573.3959182336236.5348690956
72.116398139840.01708676821250.896204157491.63518945137-0.421232613051.733784230960.04210235769350.0849498679122-0.0360508210129-0.0510827523128-0.0812295517951-0.0423881899136-0.0223089629334-0.0002497492022610.01193375228860.1828460883480.01216817369510.01644189196140.201418655671-0.006527414595730.19015165772734.32286415384.5147732218530.9082842583
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 190 through 265 )AA190 - 2651 - 61
22chain 'A' and (resid 266 through 318 )AA266 - 31862 - 114
33chain 'A' and (resid 319 through 378 )AA319 - 378115 - 174
44chain 'B' and (resid 190 through 222 )BF190 - 2221 - 33
55chain 'B' and (resid 223 through 265 )BF223 - 26534 - 60
66chain 'B' and (resid 266 through 309 )BF266 - 30961 - 104
77chain 'B' and (resid 310 through 378 )BF310 - 378105 - 173

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