[English] 日本語
Yorodumi
- PDB-5cqk: Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cqk
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 / 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 / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon 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
TRIETHYLENE GLYCOL / DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsShi, K. / Kurahashi, K. / Aihara, H.
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, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,5527
Polymers21,9791
Non-polymers5736
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.630, 54.040, 66.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
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 / 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

-
Non-polymers , 5 types, 99 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MES-NaOH

-
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: Jul 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→42 Å / Num. obs: 13173 / % possible obs: 98 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.207 / Net I/σ(I): 10.4
Reflection shellResolution: 1.88→1.95 Å / Rmerge(I) obs: 0.168

-
Processing

Software
NameVersionClassification
PHENIX(dev_2166: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQD

5cqd


Resolution: 1.88→41.918 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 701 5 %
Rwork0.1736 --
obs0.1751 13173 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→41.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 34 93 1625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091576
X-RAY DIFFRACTIONf_angle_d0.9722127
X-RAY DIFFRACTIONf_dihedral_angle_d15.361929
X-RAY DIFFRACTIONf_chiral_restr0.055216
X-RAY DIFFRACTIONf_plane_restr0.007275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8801-1.94730.35021350.31492664X-RAY DIFFRACTION96
1.9473-2.02520.29821450.2822640X-RAY DIFFRACTION98
2.0252-2.11740.27011260.2372683X-RAY DIFFRACTION99
2.1174-2.2290.23451420.21682650X-RAY DIFFRACTION99
2.229-2.36870.23671510.19962731X-RAY DIFFRACTION99
2.3687-2.55150.24371490.17962692X-RAY DIFFRACTION99
2.5515-2.80820.23771300.16092689X-RAY DIFFRACTION99
2.8082-3.21450.19051490.14932699X-RAY DIFFRACTION99
3.2145-4.04940.14841390.12222681X-RAY DIFFRACTION99
4.0494-41.92880.1491460.14422671X-RAY DIFFRACTION98
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)
10.22730.22480.16660.31230.12990.50710.00580.1344-0.0772-0.05320.1347-0.01810.20540.30590.08770.14360.0254-0.0040.1679-0.02460.1654-0.1677-17.10472.158
20.0618-0.00490.00640.0292-0.03050.1515-0.06180.0953-0.0917-0.04010.02010.2115-0.14490.0207-0.05240.15340.0474-0.00770.1420.00910.1907-10.9378-0.59410.6916
30.01430.0277-0.0320.1542-0.02210.114-0.0733-0.0539-0.024-0.15130.01560.0666-0.05680.0346-0.02140.12370.0012-0.02690.12170.0090.1247-10.66551.1085-3.0646
40.1485-0.0503-0.11690.06470.00740.1132-0.1301-0.02480.110.12770.0362-0.1459-0.12650.2645-0.00220.1633-0.02320.00960.1536-0.01220.13840.88-0.33838.2611
50.10.0211-0.09260.1553-0.06090.1466-0.0452-0.1444-0.02740.1016-0.00450.1854-0.17140.0447-0.01720.14280.0065-0.02950.1006-0.0120.1895-12.3893.88774.2761
60.39730.0440.08990.0618-0.04820.11140.0466-0.1349-0.0254-0.0604-0.00510.0145-0.2489-0.13880.03670.20330.03940.02270.1145-0.01680.1316-8.3393-2.416114.1873
70.06140.10340.03520.16320.07560.08510.0999-0.0377-0.09750.2391-0.0356-0.02220.0693-0.03110.01150.17590.01250.02060.1554-0.01940.1613-8.2532-12.826218.9403
80.105-0.05350.03210.3366-0.0510.0559-0.06650.12920.065-0.00920.06870.180.0278-0.0750.01130.1207-0.0140.01780.18210.01810.1425-12.5955-12.57210.7106
90.0617-0.0615-0.04180.1726-0.00630.046-0.12460.2083-0.09510.02520.19490.05040.09320.19610.00550.1995-0.04880.01080.2546-0.03790.1688-6.2777-19.6654-8.2855
100.06550.0373-0.02410.028-00.02170.06-0.0463-0.24940.0782-0.11440.05280.1611-0.22200.1814-0.0118-0.00680.18440.00630.1517-16.1145-20.505811.9129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 190:214 )A190 - 214
2X-RAY DIFFRACTION2( CHAIN A AND RESID 215:224 )A215 - 224
3X-RAY DIFFRACTION3( CHAIN A AND RESID 225:239 )A225 - 239
4X-RAY DIFFRACTION4( CHAIN A AND RESID 240:265 )A240 - 265
5X-RAY DIFFRACTION5( CHAIN A AND RESID 266:279 )A266 - 279
6X-RAY DIFFRACTION6( CHAIN A AND RESID 280:309 )A280 - 309
7X-RAY DIFFRACTION7( CHAIN A AND RESID 310:328 )A310 - 328
8X-RAY DIFFRACTION8( CHAIN A AND RESID 329:348 )A329 - 348
9X-RAY DIFFRACTION9( CHAIN A AND RESID 349:361 )A349 - 361
10X-RAY DIFFRACTION10( CHAIN A AND RESID 362:378 )A362 - 378

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more