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- PDB-6k0c: Crystal structure of ceNAP1-H2A.Z-H2B complex -

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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


: / HATs acetylate histones / : / Estrogen-dependent gene expression / negative regulation of cell fate specification / : / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / : / Transcriptional regulation by small RNAs ...: / HATs acetylate histones / : / Estrogen-dependent gene expression / negative regulation of cell fate specification / : / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / : / Transcriptional regulation by small RNAs / : / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / Formation of the beta-catenin:TCF transactivating complex / heterochromatin formation => GO:0031507 / cholesterol binding / condensed chromosome / nucleosome assembly / nucleosome / 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 / 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 H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350

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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

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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

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