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- PDB-7w5m: Crystal structure of AtNASP in complex of H3 alpha3 helix peptide -

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Basic information

Entry
Database: PDB / ID: 7w5m
TitleCrystal structure of AtNASP in complex of H3 alpha3 helix peptide
Components
  • H3 alpha3 helix peptide
  • Tetratricopeptide repeat (TPR)-like superfamily protein
KeywordsCHAPERONE / Histone chaperone
Function / homology
Function and homology information


CENP-A containing chromatin assembly / DNA replication-dependent chromatin assembly / 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 ...CENP-A containing chromatin assembly / DNA replication-dependent chromatin assembly / 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 / histone binding / 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
TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 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 / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Histone H3.3 / Tetratricopeptide repeat (TPR)-like superfamily protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLiu, Y. / Bao, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800619 China
CitationJournal: J Integr Plant Biol / Year: 2022
Title: Structural basis for histone H3 recognition by NASP in Arabidopsis.
Authors: Liu, Y. / Chen, L. / Wang, N. / Wu, B. / Bao, H. / Huang, H.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Jan 11, 2023Group: 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
A: Tetratricopeptide repeat (TPR)-like superfamily protein
B: H3 alpha3 helix peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7248
Polymers31,9552
Non-polymers7696
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-40 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.278, 62.803, 92.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Tetratricopeptide repeat (TPR)-like superfamily protein / Uncharacterized protein At4g37210


Mass: 29569.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AP22.13, AP22_13, At4g37210 / Production host: Escherichia coli (E. coli) / References: UniProt: Q94K88
#2: Protein/peptide H3 alpha3 helix peptide


Mass: 2385.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243

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Non-polymers , 4 types, 67 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% PEG 300, 0.2M Ammonium sulfate, 0.1M Phosphate citrate, pH 4.2, 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03314 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03314 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 16876 / % possible obs: 99.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 34.27 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.046 / Rrim(I) all: 0.108 / Χ2: 0.427 / Net I/σ(I): 3.2 / Num. measured all: 88647
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.234.70.66516110.6880.330.7460.41597.4
2.23-2.325.10.49616560.8570.2390.5530.43399.7
2.32-2.425.20.41616590.8940.20.4620.43699.9
2.42-2.555.40.30416590.9470.1430.3370.47899.8
2.55-2.715.60.25316900.9530.1170.2790.447100
2.71-2.925.30.1816670.9780.0850.1990.44399.9
2.92-3.215.40.12616960.9890.0590.1390.4499.8
3.21-3.685.50.07917000.9950.0370.0880.42899.9
3.68-4.635.30.05117190.9970.0240.0570.40599.7
4.63-4050.0418190.9990.0190.0450.34499

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V1M

7v1m


Resolution: 2.15→31.401 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 854 5.09 %
Rwork0.1842 15938 -
obs0.1863 16792 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.34 Å2 / Biso mean: 43.4324 Å2 / Biso min: 19.19 Å2
Refinement stepCycle: final / Resolution: 2.15→31.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 47 61 2006
Biso mean--61.2 48.39 -
Num. residues----242
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.28470.28441430.2168255398
2.2847-2.4610.27171590.21092627100
2.461-2.70860.26721220.1992649100
2.7086-3.10020.26431500.18692636100
3.1002-3.90480.20751270.17222701100
3.9048-31.40.1951530.1753277299
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)
13.27553.3222-3.66773.8187-4.8938.72710.2999-0.05920.68321.23550.07270.3844-1.6545-0.3781-0.4120.53780.04090.03130.3509-0.04590.3774-11.503217.071714.274
24.0881-1.6975-1.17754.45831.14525.0407-0.1425-0.30180.0330.63680.0395-0.22240.1370.16910.12610.2592-0.0304-0.03040.24980.04140.259.40112.947928.8695
36.30261.60290.66396.71020.11434.0569-0.0330.0514-0.225-0.00790.06450.05630.0960.0469-0.01890.15050.04150.02210.2244-0.01090.20591.27976.930212.8075
45.73011.5334-2.26655.5302-4.09027.2269-0.09840.0306-0.3124-0.23020.06670.22540.2639-0.24040.03790.21570.0302-0.05040.2768-0.02430.243-12.76127.26236.9577
54.24682.6578-5.03844.5344-5.84147.06530.18540.12720.00930.34660.15710.2671-0.6503-0.538-0.36890.3313-0.0115-0.0720.39730.03250.4431-16.339714.24882.1853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 118 through 132 )B118 - 132
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 231 )A75 - 231
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 278 )A232 - 278
4X-RAY DIFFRACTION4chain 'A' and (resid 279 through 354 )A279 - 354
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 394 )A355 - 394

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