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- PDB-7v1l: Structure of sNASP core in complex with H3 alpha3 helix peptide -

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Basic information

Entry
Database: PDB / ID: 7v1l
TitleStructure of sNASP core in complex with H3 alpha3 helix peptide
Components
  • H3 alpha3 helix peptide
  • Isoform 2 of Nuclear autoantigenic sperm protein
KeywordsCHAPERONE / histone chaperone
Function / homology
Function and homology information


nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) ...nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Isoform 2 of Nuclear autoantigenic sperm protein / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.849 Å
AuthorsBao, H. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFC1004500 China
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: NASP maintains histone H3-H4 homeostasis through two distinct H3 binding modes.
Authors: Bao, H. / Carraro, M. / Flury, V. / Liu, Y. / Luo, M. / Chen, L. / Groth, A. / Huang, H.
History
DepositionAug 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Isoform 2 of Nuclear autoantigenic sperm protein
V: H3 alpha3 helix peptide


Theoretical massNumber of molelcules
Total (without water)30,6482
Polymers30,6482
Non-polymers00
Water0
1
B: Isoform 2 of Nuclear autoantigenic sperm protein
V: H3 alpha3 helix peptide

B: Isoform 2 of Nuclear autoantigenic sperm protein
V: H3 alpha3 helix peptide


Theoretical massNumber of molelcules
Total (without water)61,2974
Polymers61,2974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7110 Å2
ΔGint-39 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.902, 177.051, 65.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Isoform 2 of Nuclear autoantigenic sperm protein / NASP / NASP


Mass: 28262.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence is amino acids 30 to 340 from sp P49321-2(NASP_HUMAN Isoform 2) with a deletion of amino acids 101-159.
Source: (gene. exp.) Homo sapiens (human) / Gene: NASP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P49321-2
#2: Protein/peptide H3 alpha3 helix peptide


Mass: 2385.878 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84243

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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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.4M Na-K phosphate, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9766 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 2.849→40 Å / Num. obs: 9497 / % possible obs: 99.8 % / Redundancy: 12 % / Biso Wilson estimate: 70.52 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.045 / Rrim(I) all: 0.149 / Χ2: 0.501 / Net I/σ(I): 2.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.85-2.95109260.4750.390.36398.4
2.95-3.07119090.7290.2840.37599.80.920.964
3.07-3.2111.39350.8970.2130.3961000.6960.729
3.21-3.3812.79480.9650.1360.4231000.470.49
3.38-3.5912.99300.9820.0910.45199.90.3170.33
3.59-3.8712.79490.9880.0640.5111000.2190.228
3.87-4.2611.99460.9940.0430.5721000.1450.151
4.26-4.8713.29470.9970.0310.6171000.1110.115
4.87-6.1312.19770.9960.0320.55899.90.110.114
6.13-4012.110300.9980.0180.67399.90.0590.062

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NQ0

4nq0


Resolution: 2.849→36.742 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 469 4.95 %
Rwork0.2005 9009 -
obs0.2031 9478 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.23 Å2 / Biso mean: 72.8168 Å2 / Biso min: 38.17 Å2
Refinement stepCycle: final / Resolution: 2.849→36.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 0 1852
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081875
X-RAY DIFFRACTIONf_angle_d0.9352518
X-RAY DIFFRACTIONf_chiral_restr0.04277
X-RAY DIFFRACTIONf_plane_restr0.005331
X-RAY DIFFRACTIONf_dihedral_angle_d20.0451153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.849-3.26090.32621330.2675295199
3.2609-4.10750.26361590.20192981100
4.1075-36.7420.22421770.18213077100
Refinement TLS params.Method: refined / Origin x: 56.5464 Å / Origin y: 71.4866 Å / Origin z: 39.3053 Å
111213212223313233
T0.3648 Å20.0032 Å2-0.0222 Å2-0.5185 Å2-0.0776 Å2--0.4053 Å2
L0.4604 °2-0.1042 °2-0.3423 °2-1.7221 °2-0.1341 °2--0.4202 °2
S-0.1698 Å °0.0381 Å °-0.089 Å °-0.1331 Å °0.0168 Å °-0.0184 Å °0.1071 Å °-0.1662 Å °0.1367 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB38 - 332
2X-RAY DIFFRACTION1allV120 - 133

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