[English] 日本語
Yorodumi
- PDB-4uy4: 1.86 A structure of human Spindlin-4 protein in complex with hist... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uy4
Title1.86 A structure of human Spindlin-4 protein in complex with histone H3K4me3 peptide
Components
  • HISTONE H3K4ME3
  • SPINDLIN-4
KeywordsPEPTIDE BINDING PROTEIN / SPINDLIN MEMBER 4 / SPIN4 / TUDOR DOMAIN / EPIGENETIC / CYSTICERCOSIS / MENINGOENCEPHALITIS
Function / homology
Function and homology information


gamete generation / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes ...gamete generation / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / 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 / 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 / HDMs demethylate histones / 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 / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Spindlin-4 / Spindlin/Ssty / Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...Spindlin-4 / Spindlin/Ssty / Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / Spindlin-4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.862 Å
AuthorsTalon, R. / Gileadi, C. / Johansson, C. / Burgess-Brown, N. / Shrestha, L. / von Delft, F. / Krojer, T. / Fairhead, M. / Bountra, C. / Arrowsmith, C.H. ...Talon, R. / Gileadi, C. / Johansson, C. / Burgess-Brown, N. / Shrestha, L. / von Delft, F. / Krojer, T. / Fairhead, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: 1.86 A Structure of Human Spindlin-4 Protein in Complex with Histone H3K4Me3 Peptide
Authors: Talon, R. / Gileadi, C. / Johansson, C. / Burgess-Brown, N. / Shrestha, L. / Fairhead, M. / von Delft, F. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U.
History
DepositionAug 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3May 15, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SPINDLIN-4
B: SPINDLIN-4
C: HISTONE H3K4ME3
D: HISTONE H3K4ME3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3535
Polymers51,2604
Non-polymers921
Water3,531196
1
B: SPINDLIN-4
D: HISTONE H3K4ME3


Theoretical massNumber of molelcules
Total (without water)25,6302
Polymers25,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-3.7 kcal/mol
Surface area11990 Å2
MethodPISA
2
A: SPINDLIN-4
C: HISTONE H3K4ME3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7223
Polymers25,6302
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-3.9 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.072, 51.690, 57.141
Angle α, β, γ (deg.)81.25, 89.89, 88.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (1, 0.0003, -0.0036), (0.0002, -1, -0.0044), (-0.0036, 0.0044, -1)
Vector: 17.7773, 28.545, 21.1581)

-
Components

#1: Protein SPINDLIN-4


Mass: 24882.346 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 36-249
Source method: isolated from a genetically manipulated source
Details: HISTIDINE TAG CLEAVED, THE NUMBERING START AT THR36
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q56A73
#2: Protein/peptide HISTONE H3K4ME3


Mass: 747.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431*PLUS
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MODEL CONTAINS RESIDUE T36 TO V236

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7 / Details: 33% PEG3350, 0.1M HEPES PH 7.0, SEEDING, 20C

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 17, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.21
ReflectionResolution: 1.86→28.68 Å / Num. obs: 35908 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 29.23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9
Reflection shellResolution: 1.86→5.89 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 91.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MZF LONGEST CHAIN POLY ALA CONVERTED

4mzf


Resolution: 1.862→28.683 Å / SU ML: 0.27 / σ(F): 0.75 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1803 5 %
Rwork0.2016 --
obs0.2033 35879 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.05 Å2
Refinement stepCycle: LAST / Resolution: 1.862→28.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 6 196 3547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073523
X-RAY DIFFRACTIONf_angle_d1.034811
X-RAY DIFFRACTIONf_dihedral_angle_d13.2121282
X-RAY DIFFRACTIONf_chiral_restr0.053535
X-RAY DIFFRACTIONf_plane_restr0.005608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.862-1.91230.43431290.34262313X-RAY DIFFRACTION87
1.9123-1.96860.37471330.29312644X-RAY DIFFRACTION97
1.9686-2.03210.2981380.25992579X-RAY DIFFRACTION97
2.0321-2.10470.25141430.23922615X-RAY DIFFRACTION97
2.1047-2.1890.27891390.24362638X-RAY DIFFRACTION97
2.189-2.28860.30031360.23082662X-RAY DIFFRACTION98
2.2886-2.40920.25991400.23052614X-RAY DIFFRACTION98
2.4092-2.560.23441360.23052669X-RAY DIFFRACTION98
2.56-2.75750.26381470.23092644X-RAY DIFFRACTION98
2.7575-3.03470.22761370.21292681X-RAY DIFFRACTION98
3.0347-3.47320.21011430.19052648X-RAY DIFFRACTION99
3.4732-4.37340.20081450.16442690X-RAY DIFFRACTION99
4.3734-28.68680.20461370.16562679X-RAY DIFFRACTION100
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)
14.05680.786-2.80283.172-2.00568.57170.2128-0.85790.63130.1831-0.44080.9299-1.62390.5977-0.74510.20470.07850.13161.0618-0.41410.485336.08493.527146.7228
23.3268-0.1630.28872.87220.66653.1297-0.56040.13691.2173-1.4698-0.18630.3456-2.02480.7288-0.52231.1820.3408-0.3025-0.1506-0.15290.784550.323613.552732.3149
34.805-0.062-0.23295.33321.33384.6874-0.1685-0.47370.8515-0.4615-0.33670.243-1.24-0.58810.31340.49790.1358-0.12320.3252-0.12970.381643.70396.024234.7757
46.08950.52891.61273.56131.22834.1798-0.3120.83910.3964-1.0586-0.2220.3892-1.0796-0.84370.28030.59330.1392-0.14450.6127-0.01450.291636.5531-2.106614.9195
54.2737-4.775-4.07817.35613.81062.0204-0.4664-1.4207-1.48240.48630.17850.72371.68291.0580.90190.43310.01940.05630.74530.10860.560449.0768-19.952628.6799
66.9471-0.6589-1.24083.37091.05876.2118-0.03560.1408-0.2184-0.06060.1732-0.20930.10030.3142-0.03070.13650.00340.02180.2552-0.03540.182549.8347-10.212628.1681
77.59021.8033.51165.77680.10921.69460.22861.1698-0.2708-0.3092-0.1515-0.01511.27740.1813-0.01110.29380.0742-0.02390.476-0.09640.32318.364125.1227-25.4681
84.7681-4.0868-1.04285.509-1.38653.2753-0.0204-0.0946-0.81051.16440.1999-0.68752.42070.0472-0.10491.24980.3331-0.31730.2724-0.17620.600132.859914.7213-11.3444
94.9355-2.04910.66176.46221.26625.51460.07480.2231-0.62540.6309-0.1128-0.05781.3641-0.05160.0490.50990.0261-0.04140.2628-0.07080.272325.777722.7732-13.6014
105.5981-0.0413-0.8634.39971.35445.32330.0999-0.8136-0.2871.2345-0.29690.21071.3628-0.87410.15640.6838-0.17520.06240.5842-0.00240.218619.187930.04726.5429
113.22932.6701-1.30452.927-1.30494.4973-0.16160.38191.8248-0.19510.59821.3027-2.1741.050.08660.5824-0.125-0.06460.50380.09470.784830.150348.6377-7.6146
127.76721.28451.63241.652-0.36734.7060.1664-0.18580.16330.05330.1559-0.25840.08910.8539-0.17480.17950.0418-0.00250.437-0.0990.242632.038238.9553-6.9858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:26)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 27:74)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 75:154)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 155:167)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 168:215)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1:9)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 10:26)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 27:74)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 75:154)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 155:167)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 168:215)

+
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