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- PDB-4uy4: 1.86 A structure of human Spindlin-4 protein in complex with hist... -

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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 / homologySpin/Ssty Family / Core histone H2A/H2B/H3/H4 / RMTs methylate histone arginines / HATs acetylate histones / HDMs demethylate histones / Histone H3/CENP-A / Spindlin/spermiogenesis-specific protein / Histone H2A/H2B/H3 / Histone-fold / Spindlin-4 ...Spin/Ssty Family / Core histone H2A/H2B/H3/H4 / RMTs methylate histone arginines / HATs acetylate histones / HDMs demethylate histones / Histone H3/CENP-A / Spindlin/spermiogenesis-specific protein / Histone H2A/H2B/H3 / Histone-fold / Spindlin-4 / PKMTs methylate histone lysines / HDACs deacetylate histones / Histone H3 signature 1. / Histone H3 signature 2. / Interleukin-7 signaling / Pre-NOTCH Transcription and Translation / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Chromatin modifying enzymes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / NoRC negatively regulates rRNA expression / Factors involved in megakaryocyte development and platelet production / Amyloid fiber formation / Meiotic recombination / Estrogen-dependent gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RNA Polymerase I Chain Elongation / Senescence-Associated Secretory Phenotype (SASP) / RNA Polymerase I Promoter Opening / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation by small RNAs / DNA methylation / B-WICH complex positively regulates rRNA expression / gamete generation / interleukin-7-mediated signaling pathway / DNA replication-dependent nucleosome assembly / telomere organization / nuclear nucleosome / regulation of gene silencing by miRNA / chromatin silencing at rDNA / nucleosomal DNA binding / negative regulation of gene expression, epigenetic / nuclear chromosome / methylated histone binding / regulation of gene silencing / regulation of megakaryocyte differentiation / nucleosome / nucleosome assembly / protein heterotetramerization / chromatin organization / cadherin binding / blood coagulation / cellular protein metabolic process / protein heterodimerization activity / protein-containing complex / extracellular exosome / membrane / nucleoplasm / extracellular region / nucleus / cytosol / Histone H3.1 / Spindlin-4
Function and homology information
Specimen sourceHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.862 Å resolution
AuthorsTalon, 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 28, 2014 / Release: Sep 24, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 24, 2014Structure modelrepositoryInitial release
1.1Aug 19, 2015Structure modelDatabase references / Structure summary
1.2Jan 24, 2018Structure modelDatabase references / Structure summaryaudit_author / citation_author_audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Polyers51,2604
Non-polymers921
Water3,531196
1
B: SPINDLIN-4
D: HISTONE H3K4ME3


Theoretical massNumber of molelcules
Total (without water)25,6302
Polyers25,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)960
ΔGint (kcal/M)-3.7
Surface area (Å2)11990
MethodPISA
2
A: SPINDLIN-4
C: HISTONE H3K4ME3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7223
Polyers25,6302
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1170
ΔGint (kcal/M)-3.9
Surface area (Å2)11540
MethodPISA
Unit cell
γ
α
β
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-MP 1

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Components

#1: Protein/peptide SPINDLIN-4


Mass: 24882.346 Da / Num. of mol.: 2
Details: HISTIDINE TAG CLEAVED, THE NUMBERING START AT THR36
Fragment: UNP RESIDUES 36-249 / 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: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Formula: C3H8O3 / Glycerol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Formula: H2O / Water
Sequence detailsTHE MODEL CONTAINS RESIDUE T36 TO V236

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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: 2.35 / Density percent sol: 48 % / Description: NONE
Crystal growpH: 7 / Details: 33% PEG3350, 0.1M HEPES PH 7.0, SEEDING, 20C

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PIXEL / Details: MIRRORS / Detector: PIXEL / Collection date: May 17, 2014
RadiationMonochromator: DOUBLE CRYSTAL / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.21
ReflectionB iso Wilson estimate: 29.23 Å2 / D resolution high: 1.86 Å / D resolution low: 28.68 Å / Number obs: 35908 / Observed criterion sigma I: -3 / Rmerge I obs: 0.06 / NetI over sigmaI: 9 / Redundancy: 3.6 % / Percent possible obs: 97.2
Reflection shellRmerge I obs: 0.36 / Highest resolution: 1.86 Å / Lowest resolution: 5.89 Å / MeanI over sigI obs: 2.4 / Redundancy: 3.4 % / Percent possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MZF LONGEST CHAIN POLY ALA CONVERTED
Overall SU ML: 0.27 / Sigma F: 0.75 / Overall phase error: 29.02 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso mean: 49.05 Å2
Least-squares processR factor R free: 0.235 / R factor R work: 0.2016 / R factor obs: 0.2033 / Highest resolution: 1.862 Å / Lowest resolution: 28.683 Å / Number reflection R free: 1803 / Number reflection obs: 35879 / Percent reflection R free: 5 / Percent reflection obs: 97.11
Refine hist #LASTHighest resolution: 1.862 Å / Lowest resolution: 28.683 Å
Number of atoms included #LASTProtein: 3345 / Nucleic acid: 0 / Ligand: 6 / Solvent: 196 / Total: 3547
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073523
X-RAY DIFFRACTIONf_angle_d1.0304811
X-RAY DIFFRACTIONf_dihedral_angle_d13.2121282
X-RAY DIFFRACTIONf_chiral_restr0.053535
X-RAY DIFFRACTIONf_plane_restr0.005608
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.86200.43430.34261.9123129231387.00
1.91230.37470.29311.9686133264497.00
1.96860.29800.25992.0321138257997.00
2.03210.25140.23922.1047143261597.00
2.10470.27890.24362.1890139263897.00
2.18900.30030.23082.2886136266298.00
2.28860.25990.23052.4092140261498.00
2.40920.23440.23052.5600136266998.00
2.56000.26380.23092.7575147264498.00
2.75750.22760.21293.0347137268198.00
3.03470.21010.19053.4732143264899.00
3.47320.20080.16444.3734145269099.00
4.37340.20460.165628.68681372679100.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
14.05680.7860-2.80283.1720-2.00568.57170.2128-0.85790.63130.1831-0.44080.9299-1.62390.5977-0.74510.20470.07850.13161.0618-0.41410.485336.08493.527146.7228
23.3268-0.16300.28872.87220.66653.1297-0.56040.13691.2173-1.4698-0.18630.3456-2.02480.7288-0.52231.18200.3408-0.3025-0.1506-0.15290.784550.323613.552732.3149
34.8050-0.0620-0.23295.33321.33384.6874-0.1685-0.47370.8515-0.4615-0.33670.2430-1.2400-0.58810.31340.49790.1358-0.12320.3252-0.12970.381643.70396.024234.7757
46.08950.52891.61273.56131.22834.1798-0.31200.83910.3964-1.0586-0.22200.3892-1.0796-0.84370.28030.59330.1392-0.14450.6127-0.01450.291636.5531-2.106614.9195
54.2737-4.7750-4.07817.35613.81062.0204-0.4664-1.4207-1.48240.48630.17850.72371.68291.05800.90190.43310.01940.05630.74530.10860.560449.0768-19.952628.6799
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
77.59021.80303.51165.77680.10921.69460.22861.1698-0.2708-0.3092-0.1515-0.01511.27740.1813-0.01110.29380.0742-0.02390.4760-0.09640.323018.364125.1227-25.4681
84.7681-4.0868-1.04285.5090-1.38653.2753-0.0204-0.0946-0.81051.16440.1999-0.68752.42070.0472-0.10491.24980.3331-0.31730.2724-0.17620.600132.859914.7213-11.3444
94.9355-2.04910.66176.46221.26625.51460.07480.2231-0.62540.6309-0.1128-0.05781.3641-0.05160.04900.50990.0261-0.04140.2628-0.07080.272325.777722.7732-13.6014
105.5981-0.0413-0.86304.39971.35445.32330.0999-0.8136-0.28701.2345-0.29690.21071.3628-0.87410.15640.6838-0.17520.06240.5842-0.00240.218619.187930.04726.5429
113.22932.6701-1.30452.9270-1.30494.4973-0.16160.38191.8248-0.19510.59821.3027-2.17401.05000.08660.5824-0.1250-0.06460.50380.09470.784830.150348.6377-7.6146
127.76721.28451.63241.6520-0.36734.70600.1664-0.18580.16330.05330.1559-0.25840.08910.8539-0.17480.17950.0418-0.00250.4370-0.09900.242632.038238.9553-6.9858
Refine 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)

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