[English] 日本語
Yorodumi
- PDB-6oe7: Crystal structure of HMCES cross-linked to DNA abasic site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oe7
TitleCrystal structure of HMCES cross-linked to DNA abasic site
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*(DRZ)P*GP*TP*T)-3')
  • DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
  • Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
KeywordsDNA BINDING PROTEIN/DNA / SRAP Domain / DNA-binding / Structural Genomics / Structural Genomics Consortium / SGC / HMCES / Protein-DNA complex / DNA damage protein / 3' overhang / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


protein-DNA covalent cross-linking activity / Lyases / DNA-(abasic site) binding / positive regulation of isotype switching / double-strand break repair via alternative nonhomologous end joining / protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / somatic hypermutation of immunoglobulin genes / interstrand cross-link repair / replication fork ...protein-DNA covalent cross-linking activity / Lyases / DNA-(abasic site) binding / positive regulation of isotype switching / double-strand break repair via alternative nonhomologous end joining / protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / somatic hypermutation of immunoglobulin genes / interstrand cross-link repair / replication fork / peptidase activity / single-stranded DNA binding / DNA damage response / proteolysis
Similarity search - Function
SOS response associated peptidase-like / hypothetical protein yedk fold / SOS response associated peptidase (SRAP) / SOS response associated peptidase-like / SOS response associated peptidase (SRAP) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Abasic site processing protein HMCES
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsHalabelian, L. / Li, Y. / Zeng, H. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.
Authors: Halabelian, L. / Ravichandran, M. / Li, Y. / Zeng, H. / Rao, A. / Aravind, L. / Arrowsmith, C.H.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
C: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*(DRZ)P*GP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,36712
Polymers37,0573
Non-polymers3109
Water59433
1
A: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
C: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*(DRZ)P*GP*TP*T)-3')
hetero molecules

C: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*(DRZ)P*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)42,75315
Polymers42,4435
Non-polymers31010
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444-x-1/2,y-1/2,-z-1/21
Unit cell
Length a, b, c (Å)55.509, 51.534, 149.720
Angle α, β, γ (deg.)90.000, 92.720, 90.000
Int Tables number5
Space group name H-MI121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein / ES cell-specific 5hmC-binding protein / Putative peptidase SRAPD1 / SRAP domain-containing protein 1


Mass: 31671.617 Da / Num. of mol.: 1 / Fragment: SRAP domain (UNP residues 2-270)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMCES, C3orf37, DC12, SRAPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96FZ2

-
DNA chain , 2 types, 2 molecules CB

#2: DNA chain DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')


Mass: 1840.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*(DRZ)P*GP*TP*T)-3')


Mass: 3545.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 42 molecules

#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG3350, 0.1 M potassium chloride, 0.1 M Bis-Tris, 0.05 M magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 15, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→48.72 Å / Num. obs: 20951 / % possible obs: 96.8 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.273.40.86118140.8180.5471.02398
9.07-48.723.10.033070.9950.0220.03891.7

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→48.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.014 / SU ML: 0.159 / SU R Cruickshank DPI: 0.2117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.17
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1036 4.9 %RANDOM
Rwork0.1942 ---
obs0.1954 19914 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.01 Å2 / Biso mean: 56.937 Å2 / Biso min: 35.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å2-0 Å2-1.5 Å2
2--3.11 Å20 Å2
3----5.11 Å2
Refinement stepCycle: final / Resolution: 2.2→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 122 184 33 2402
Biso mean--61.59 54.44 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122444
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182039
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.5913371
X-RAY DIFFRACTIONr_angle_other_deg1.3691.6954738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4915256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74721.186118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17515327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7031518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02541
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 75 -
Rwork0.344 1458 -
all-1533 -
obs--97.71 %

+
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://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