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- PDB-6k09: Crystal structure B of ceNAP1-H2A-H2B complex -

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Basic information

Entry
Database: PDB / ID: 6k09
TitleCrystal structure B of ceNAP1-H2A-H2B complex
Components
  • Histone H2B 1,Histone H2A
  • Nucleosome Assembly Protein
KeywordsCHAPERONE / NAP1 / H2A-H2B
Function / homology
Function and homology information


Metalloprotease DUBs / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / 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 ...Metalloprotease DUBs / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / 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 / Ub-specific processing proteases / cholesterol binding / nucleosomal DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / protein-containing complex binding / chromatin / DNA binding / nucleus / metal ion binding / 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
Histone H2B 1 / Histone H2A / Nucleosome assembly protein 1-like 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 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
A: Nucleosome Assembly Protein
B: Nucleosome Assembly Protein
D: Histone H2B 1,Histone H2A


Theoretical massNumber of molelcules
Total (without water)92,6323
Polymers92,6323
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint-62 kcal/mol
Surface area34110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.795, 79.180, 172.340
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 104 or (resid 105...
21(chain B and (resid 6 through 92 or (resid 93...

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 104 or (resid 105...AA6 - 10418 - 116
12GLUGLUALAALA(chain A and (resid 6 through 104 or (resid 105...AA105 - 106117 - 118
13PHEPHEASPASP(chain A and (resid 6 through 104 or (resid 105...AA6 - 29618 - 308
14PHEPHEASPASP(chain A and (resid 6 through 104 or (resid 105...AA6 - 29618 - 308
15PHEPHEASPASP(chain A and (resid 6 through 104 or (resid 105...AA6 - 29618 - 308
16PHEPHEASPASP(chain A and (resid 6 through 104 or (resid 105...AA6 - 29618 - 308
21PHEPHELEULEU(chain B and (resid 6 through 92 or (resid 93...BB6 - 9218 - 104
22GLUGLUGLUGLU(chain B and (resid 6 through 92 or (resid 93...BB93105
23PHEPHESERSER(chain B and (resid 6 through 92 or (resid 93...BB6 - 29418 - 306
24PHEPHESERSER(chain B and (resid 6 through 92 or (resid 93...BB6 - 29418 - 306
25PHEPHESERSER(chain B and (resid 6 through 92 or (resid 93...BB6 - 29418 - 306
26PHEPHESERSER(chain B and (resid 6 through 92 or (resid 93...BB6 - 29418 - 306

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Components

#1: 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) / Gene: nap-1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q19007
#2: Protein Histone H2B 1,Histone H2A


Mass: 22653.262 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: P04255, UniProt: P09588
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 51.45 %
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: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.248→49.723 Å / Num. obs: 45336 / % possible obs: 99.4 % / Redundancy: 11 % / Net I/σ(I): 25.14
Reflection shellResolution: 2.248→2.33 Å / Rmerge(I) obs: 0.557 / Num. unique obs: 45336

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Processing

Software
NameVersionClassification
PHENIX1.14_3260: ???refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.248→49.723 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.09
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2485 2205 4.86 %
Rwork0.2141 --
obs0.2157 45336 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.62 Å2 / Biso mean: 44.9284 Å2 / Biso min: 22.81 Å2
Refinement stepCycle: final / Resolution: 2.248→49.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 0 116 5716
Biso mean---38.31 -
Num. residues----715
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1556X-RAY DIFFRACTION6.211TORSIONAL
12B1556X-RAY DIFFRACTION6.211TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2479-2.29680.29441360.25552680281699
2.2968-2.35020.29281530.247926232776100
2.3502-2.4090.2971490.231626402789100
2.409-2.47420.27071300.24042659278998
2.4742-2.5470.29711430.23152650279399
2.547-2.62920.28061310.233626652796100
2.6292-2.72310.27341370.243926892826100
2.7231-2.83210.29861190.247727232842100
2.8321-2.9610.27731470.244226462793100
2.961-3.11710.26731380.24082689282799
3.1171-3.31240.23651330.23532643277697
3.3124-3.5680.27271350.23227102845100
3.568-3.9270.24081390.199527272866100
3.927-4.49490.21141350.174827412876100
4.4949-5.66180.23191240.18352769289399
5.6618-49.73540.21211560.20032877303399
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)
1-0.0033-0.25320.04291.037-0.01370.66210.0339-0.0428-0.02380.0594-0.01860.14680.01740.006-0.01130.2627-0.0406-0.00740.2996-0.00360.31457.2003-19.5844-30.88
20.3723-0.7537-0.10361.76880.19730.5925-0.0498-0.10840.01960.19630.0819-0.1292-0.14690.0406-0.04290.3066-0.0274-0.03410.27660.02450.22477.40697.0133-25.3788
32.29890.6429-0.52212.6679-0.80343.5989-0.0511-0.1028-0.08430.0634-0.00910.09840.03850.06180.07170.3085-0.0031-0.05840.46880.1040.376830.0572-21.2513-8.2504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 296)A6 - 296
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 294)B6 - 294
3X-RAY DIFFRACTION3(chain 'D' and resid 30 through 215)D30 - 215

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