[English] 日本語
Yorodumi
- PDB-4ouc: Structure of human haspin in complex with histone H3 substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ouc
TitleStructure of human haspin in complex with histone H3 substrate
Components
  • Histone H3.2
  • Serine/threonine-protein kinase haspin
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / histone / kinase substrate complex / Chromatin regulator
Function / homology
Function and homology information


protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / Chromatin modifying enzymes / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes ...protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / Chromatin modifying enzymes / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / 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 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / mitotic cell cycle / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein heterodimerization activity / Amyloid fiber formation / protein serine kinase activity / centrosome / DNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown 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 ...Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5ID / IODIDE ION / Histone H3.2 / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2014
Title: Modulation of the chromatin phosphoproteome by the haspin protein kinase.
Authors: Maiolica, A. / de Medina-Redondo, M. / Schoof, E.M. / Chaikuad, A. / Villa, F. / Gatti, M. / Jeganathan, S. / Lou, H.J. / Novy, K. / Hauri, S. / Toprak, U.H. / Herzog, F. / Meraldi, P. / ...Authors: Maiolica, A. / de Medina-Redondo, M. / Schoof, E.M. / Chaikuad, A. / Villa, F. / Gatti, M. / Jeganathan, S. / Lou, H.J. / Novy, K. / Hauri, S. / Toprak, U.H. / Herzog, F. / Meraldi, P. / Penengo, L. / Turk, B.E. / Knapp, S. / Linding, R. / Aebersold, R.
History
DepositionFeb 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase haspin
B: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,04111
Polymers42,1262
Non-polymers9149
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint5 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.540, 79.130, 100.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

-
Components

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

#1: Protein Serine/threonine-protein kinase haspin / Germ cell-specific gene 2 protein / H-haspin / Haploid germ cell-specific nuclear protein kinase


Mass: 40711.484 Da / Num. of mol.: 1 / Fragment: UNP residues 465-798
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSG2 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-R3-pRARE2
References: UniProt: Q8TF76, non-specific serine/threonine protein kinase
#2: Protein/peptide Histone H3.2 / Histone H3/m / Histone H3/o


Mass: 1414.610 Da / Num. of mol.: 1 / Fragment: histone H3 tail, UNP residues 2-13 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3

-
Non-polymers , 5 types, 428 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13IN4O4
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M potassium thiocyanate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 23, 2012
RadiationMonochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→33.59 Å / Num. all: 32592 / Num. obs: 32539 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4675 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3IQ7

3iq7


Resolution: 1.9→31.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.185 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.134 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21075 1647 5.1 %RANDOM
Rwork0.16393 ---
obs0.16628 30891 99.83 %-
all-32539 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 46 419 3150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192860
X-RAY DIFFRACTIONr_bond_other_d0.0010.022746
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9823859
X-RAY DIFFRACTIONr_angle_other_deg0.8043.0026322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98324.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06915520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.841514
X-RAY DIFFRACTIONr_chiral_restr0.1020.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02650
X-RAY DIFFRACTIONr_mcbond_it1.0721.4731358
X-RAY DIFFRACTIONr_mcbond_other1.0721.4721357
X-RAY DIFFRACTIONr_mcangle_it1.5912.2011698
X-RAY DIFFRACTIONr_mcangle_other1.592.2031699
X-RAY DIFFRACTIONr_scbond_it1.742.6891502
X-RAY DIFFRACTIONr_scbond_other1.7392.6881503
X-RAY DIFFRACTIONr_scangle_other2.7192.4572154
X-RAY DIFFRACTIONr_long_range_B_refined6.49614.5333623
X-RAY DIFFRACTIONr_long_range_B_other6.50614.5333612
X-RAY DIFFRACTIONr_sphericity_free47.94351
X-RAY DIFFRACTIONr_sphericity_bonded22.93951
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 131 -
Rwork0.283 2237 -
obs--99.66 %
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)
11.2376-0.52031.17682.6615-0.19213.1697-0.01480.1931-0.0685-0.239-0.01270.11580.08850.06880.02750.0352-0.0186-0.00840.04950.00210.042934.391534.25328.3415
21.28340.5370.58810.93440.50721.070.01280.0566-0.0512-0.05230.0277-0.02550.01010.0505-0.04040.01090.00450.0090.00550.00370.02144.433540.540317.4319
33.27240.0749-0.66841.65431.41575.511-0.0960.45180.227-0.36490.0760.0328-0.34180.06850.020.1219-0.0458-0.02230.07560.04180.045850.366455.8811.4298
43.37940.4786-2.56210.5426-0.35084.27250.1025-0.21380.11970.1824-0.01040.0099-0.23020.129-0.09210.07590.002-0.00350.0162-0.01430.055552.145456.212932.9894
511.0566.2521-11.20347.98970.210120.98030.22061.05061.1604-0.4060.17531.2241-1.1059-1.6115-0.3960.21630.0341-0.06160.19020.06640.311535.402553.977910.795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A470 - 530
2X-RAY DIFFRACTION2A531 - 694
3X-RAY DIFFRACTION3A695 - 754
4X-RAY DIFFRACTION4A755 - 798
5X-RAY DIFFRACTION5B1 - 7

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more