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- PDB-7v1m: Structural basis for the co-chaperone relationship of sNASP and ASF1b -

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Basic information

Entry
Database: PDB / ID: 7v1m
TitleStructural basis for the co-chaperone relationship of sNASP and ASF1b
Components
  • Histone H3.3H3F3A
  • Histone H4
  • Histone chaperone ASF1B
  • Isoform 2 of Nuclear autoantigenic sperm protein
KeywordsCHAPERONE / histone chaperone
Function / homology
Function and homology information


histone chaperone activity / blastocyst hatching / DNA replication-dependent chromatin assembly / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...histone chaperone activity / blastocyst hatching / DNA replication-dependent chromatin assembly / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / 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 / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor ...Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 H4 / Histone H3.3 / Histone chaperone ASF1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.834 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

Downloads & links

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Assembly

Deposited unit
B: Histone H3.3
C: Histone H4
D: Histone chaperone ASF1B
A: Histone H3.3
E: Histone H4
F: Histone chaperone ASF1B
G: Isoform 2 of Nuclear autoantigenic sperm protein
H: Isoform 2 of Nuclear autoantigenic sperm protein


Theoretical massNumber of molelcules
Total (without water)141,9698
Polymers141,9698
Non-polymers00
Water0
1
B: Histone H3.3
C: Histone H4
D: Histone chaperone ASF1B
H: Isoform 2 of Nuclear autoantigenic sperm protein


Theoretical massNumber of molelcules
Total (without water)70,9854
Polymers70,9854
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone H3.3
E: Histone H4
F: Histone chaperone ASF1B
G: Isoform 2 of Nuclear autoantigenic sperm protein


Theoretical massNumber of molelcules
Total (without water)70,9854
Polymers70,9854
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.951, 71.896, 93.427
Angle α, β, γ (deg.)70.670, 70.640, 83.610
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Histone H3.3 / H3F3A


Mass: 15229.787 Da / Num. of mol.: 2
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
#2: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P62805
#3: Protein Histone chaperone ASF1B / Anti-silencing function protein 1 homolog B / hAsf1 / hAsf1b / CCG1-interacting factor A-II / CIA-II / hCIA-II


Mass: 17915.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1B
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9NVP2
#4: Protein Isoform 2 of Nuclear autoantigenic sperm protein / NASP


Mass: 26576.592 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence is amino acids 30 to 323 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
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.5
ReflectionResolution: 2.834→40 Å / Num. obs: 37598 / % possible obs: 95.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.06 / Rrim(I) all: 0.118 / Χ2: 0.591 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.953.30.75235630.6060.4710.890.44791.3
2.95-3.073.50.57237490.760.3480.6710.45495
3.07-3.213.70.44938420.8580.2670.5230.4798
3.21-3.383.70.2938130.9350.1720.3380.47197.1
3.38-3.593.60.18638540.9670.1110.2170.51696.7
3.59-3.873.50.1336690.980.080.1530.56394.1
3.87-4.263.70.09138190.990.0540.1060.60196.4
4.26-4.873.70.07438140.9910.0440.0860.72797.7
4.87-6.133.60.06836890.9920.0410.080.71193.7
6.13-403.70.05837860.9930.0350.0680.9196.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V1L, 5BNX

7v1l

5bnx


Resolution: 2.834→35.588 Å / Cross valid method: THROUGHOUT / σ(F): 140.87 / Phase error: 26.67 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2403 1921 5.11 %
Rwork0.2023 35756 -
obs0.2097 37598 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.78 Å2 / Biso mean: 75.1489 Å2 / Biso min: 29.99 Å2
Refinement stepCycle: final / Resolution: 2.834→35.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7966 0 0 0 7966
Num. residues----1022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128106
X-RAY DIFFRACTIONf_angle_d1.24510950
X-RAY DIFFRACTIONf_chiral_restr0.071214
X-RAY DIFFRACTIONf_plane_restr0.0071443
X-RAY DIFFRACTIONf_dihedral_angle_d28.4262976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8347-2.91130.4371520.3382402255479
2.9113-2.99690.35771620.32072661282387
2.9969-3.09350.29731410.28042810295193
3.0935-3.2040.27061300.2662836296693
3.204-3.33210.31641540.24632813296792
3.3321-3.48360.26081400.22242808294892
3.4836-3.6670.22331300.19762775290592
3.667-3.89640.23341050.20042699280488
3.8964-4.19660.25761500.1832851300193
4.1966-4.61780.20151440.17092811295593
4.6178-5.28330.23451630.17452733289690
5.2833-6.64630.22811340.21842776291090
6.6463-31.67870.2241270.19532781290891
Refinement TLS params.Method: refined / Origin x: 18.1194 Å / Origin y: -51.2494 Å / Origin z: -34.843 Å
111213212223313233
T0.4459 Å20.1633 Å20.1456 Å2-0.4103 Å20.1116 Å2--0.4745 Å2
L0.0068 °20.1713 °2-0.342 °2--0.056 °2-0.2925 °2--0.9952 °2
S0.0201 Å °0.0062 Å °-0.0326 Å °0.0257 Å °0.0076 Å °0.0123 Å °-0.1161 Å °-0.0445 Å °0.0097 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB49 - 134
2X-RAY DIFFRACTION1allC22 - 101
3X-RAY DIFFRACTION1allD1 - 154
4X-RAY DIFFRACTION1allA60 - 134
5X-RAY DIFFRACTION1allE24 - 101
6X-RAY DIFFRACTION1allF1 - 154
7X-RAY DIFFRACTION1allG40 - 320
8X-RAY DIFFRACTION1allH38 - 320

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