[English] 日本語
Yorodumi
- PDB-6k0c: Crystal structure of ceNAP1-H2A.Z-H2B complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k0c
TitleCrystal structure of ceNAP1-H2A.Z-H2B complex
Components
  • Histone H2B 2,Histone H2A.V
  • Nucleosome Assembly Protein
KeywordsCHAPERONE / NAP1 / H2A.Z-H2B
Function / homology
Function and homology information


negative regulation of cell fate specification / Oxidative Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / nucleosomal DNA binding ...negative regulation of cell fate specification / Oxidative Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / nucleosomal DNA binding / cholesterol binding / condensed chromosome / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B ...Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleosome assembly protein 1-like 1 / Histone H2A.V / Histone H2B 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.281 Å
AuthorsLiu, Y.R.
CitationJournal: Structure / Year: 2019
Title: Crystal structure of xlH2A-H2B
Authors: Liu, Y.R.
History
DepositionMay 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Histone H2B 2,Histone H2A.V
A: Nucleosome Assembly Protein
B: Nucleosome Assembly Protein


Theoretical massNumber of molelcules
Total (without water)92,4593
Polymers92,4593
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-62 kcal/mol
Surface area34620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.728, 79.313, 174.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 216 or resid 234...
21(chain B and (resid 6 through 8 or (resid 9...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEALAALA(chain A and (resid 6 through 216 or resid 234...AB6 - 21618 - 228
12THRTHRARGARG(chain A and (resid 6 through 216 or resid 234...AB234 - 253246 - 265
13ASPASPASPASP(chain A and (resid 6 through 216 or resid 234...AB258270
14ASPASPALAALA(chain A and (resid 6 through 216 or resid 234...AB259 - 262271 - 274
15PHEPHEASPASP(chain A and (resid 6 through 216 or resid 234...AB6 - 29618 - 308
16PHEPHEASPASP(chain A and (resid 6 through 216 or resid 234...AB6 - 29618 - 308
17PHEPHEASPASP(chain A and (resid 6 through 216 or resid 234...AB6 - 29618 - 308
18PHEPHEASPASP(chain A and (resid 6 through 216 or resid 234...AB6 - 29618 - 308
21PHEPHEHISHIS(chain B and (resid 6 through 8 or (resid 9...BC6 - 818 - 20
22METMETMETMET(chain B and (resid 6 through 8 or (resid 9...BC921
23PHEPHEGLNGLN(chain B and (resid 6 through 8 or (resid 9...BC6 - 29318 - 305

-
Components

#1: Protein Histone H2B 2,Histone H2A.V / H2A.F/Z


Mass: 22481.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q27894, UniProt: Q27511
#2: Protein Nucleosome Assembly Protein


Mass: 34989.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q19007
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.28→49.394 Å / Num. obs: 43537 / % possible obs: 99.9 % / Redundancy: 6.6 % / Net I/σ(I): 14.43
Reflection shellResolution: 2.28→2.36 Å / Rmerge(I) obs: 0.642 / Num. unique obs: 43537

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.281→49.394 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2623 2137 4.91 %
Rwork0.2166 41400 -
obs0.2187 43537 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.1 Å2 / Biso mean: 53.1613 Å2 / Biso min: 22.35 Å2
Refinement stepCycle: final / Resolution: 2.281→49.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 0 106 5803
Biso mean---41.54 -
Num. residues----725
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1600X-RAY DIFFRACTION8.659TORSIONAL
12B1600X-RAY DIFFRACTION8.659TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.281-2.33410.27361510.25482705285699
2.3341-2.39250.32971440.260426692813100
2.3925-2.45720.30771510.2627072858100
2.4572-2.52950.30041430.262627262869100
2.5295-2.61110.31271400.246927612901100
2.6111-2.70440.30521360.239727192855100
2.7044-2.81270.30131360.246627342870100
2.8127-2.94070.29651360.244227552891100
2.9407-3.09570.27121520.252227282880100
3.0957-3.28960.28681350.233327522887100
3.2896-3.54350.28241270.215727832910100
3.5435-3.90.2341470.202927802927100
3.9-4.4640.21421390.171727982937100
4.464-5.62290.2131390.185428452984100
5.6229-49.40540.26531610.2162938309999
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)
12.18760.1187-1.02522.7137-0.38862.8273-0.2294-0.6203-0.15850.06840.31860.18220.06050.2205-0.08720.5774-0.0104-0.04261.09280.05440.507129.5797-24.3448-8.9862
2-0.2674-0.1860.16531.22570.04780.8580.0093-0.0629-0.04010.0401-0.01860.18490.00340.04760.00950.2438-0.02240.01220.2887-0.00040.3316.7007-20.7504-30.9911
30.4108-0.3103-0.10821.12840.08340.8699-0.009-0.1150.01540.17910.0438-0.1362-0.18740.0754-0.04880.3529-0.0318-0.03140.30440.02270.27967.8486.3478-25.829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'D' and resid 29 through 212)D29 - 212
2X-RAY DIFFRACTION2(chain 'A' and resid 6 through 296)A6 - 296
3X-RAY DIFFRACTION3(chain 'B' and resid 6 through 293)B6 - 293

+
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