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- PDB-5lug: Crystal structure of human Spindlin-2B protein in complex with AR... -

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Basic information

Entry
Database: PDB / ID: 5lug
TitleCrystal structure of human Spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide
Components
  • ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
  • Spindlin-like protein 2, isoform CRA_a
KeywordsCELL CYCLE / SPINDLIN-2B (protein): PEPTIDE BINDING PROTEIN / SPINDLIN MEMBER 2B / SPIN2B / TUDOR DOMAIN
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 / regulation of cell cycle / cadherin binding / cell cycle / Amyloid fiber formation / protein heterodimerization activity / apoptotic process / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Spindlin-2 / Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / 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
N3, N4-DIMETHYLARGININE / Spindlin-like protein 2, isoform CRA_a / Histone H3.1 / Spindlin-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsSrikannathasan, V. / Gileadi, C. / Talon, R. / Shrestha, L. / Kopec, J. / Szykowska, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Srikannathasan, V. / Gileadi, C. / Talon, R. / Shrestha, L. / Kopec, J. / Szykowska, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Oppermann, U. / Huber, K.
CitationJournal: To be published
Title: Crystal structure of human Spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide
Authors: Srikannathasan, V.
History
DepositionSep 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindlin-like protein 2, isoform CRA_a
B: Spindlin-like protein 2, isoform CRA_a
C: Spindlin-like protein 2, isoform CRA_a
D: Spindlin-like protein 2, isoform CRA_a
F: ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
G: ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
H: ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
E: ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,47715
Polymers106,9028
Non-polymers5757
Water14,160786
1
A: Spindlin-like protein 2, isoform CRA_a
C: Spindlin-like protein 2, isoform CRA_a
F: ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
H: ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5756
Polymers53,4514
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spindlin-like protein 2, isoform CRA_a
D: Spindlin-like protein 2, isoform CRA_a
G: ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
E: ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9019
Polymers53,4514
Non-polymers4515
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.533, 81.225, 93.967
Angle α, β, γ (deg.)90.000, 99.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid AA
21chain B and segid BA
31chain D and segid DA

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AAA0
211chain B and segid BAB0
311chain D and segid DAD0

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Components

#1: Protein
Spindlin-like protein 2, isoform CRA_a / SPINDLIN MEMBER 2B / SPIN2B / TUDOR DOMAIN


Mass: 25506.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ART(M3L)QTA(2MR)KS peptide / Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN-2, hCG_1642309 / Plasmid: pNIC-CTHF
Details (production host): C -terminal, TEV cleavable hexahistidine tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-Rosetta / References: UniProt: A0A024R9Y9, UniProt: Q9BPZ2*PLUS
#2: Protein/peptide
ALA-ARG-THR-M3L-GLN-THR-ALA-2MR-LYS-SER


Mass: 1219.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ART(M3L)QTA(2MR)KS - co crystallised and no density for KS and 2MR show dual conformation.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-2MR / N3, N4-DIMETHYLARGININE


Type: L-peptide linking / Mass: 202.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 107508 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.071 / Rrim(I) all: 0.145 / Net I/σ(I): 11.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.9 / Num. unique all: 15448 / CC1/2: 0.88 / Rpim(I) all: 0.32 / Rrim(I) all: 0.623 / % possible all: 98.3

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.9_1682refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementResolution: 1.7→19.902 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 29.32
Details: initial refinement carried on REFMAC then later and final refinement done by PHENIX refinement; Protein residues do not have density: ESSESPPTEREPG Some residues side chain are removed due ...Details: initial refinement carried on REFMAC then later and final refinement done by PHENIX refinement; Protein residues do not have density: ESSESPPTEREPG Some residues side chain are removed due to lack of density.Some residues have dual conformation.
RfactorNum. reflection% reflection
Rfree0.2211 5304 4.94 %
Rwork0.1942 --
obs0.1956 107408 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.32 Å2 / Biso mean: 23.8694 Å2 / Biso min: 10.2 Å2
Refinement stepCycle: final / Resolution: 1.7→19.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6865 0 76 786 7727
Biso mean--43.32 31.1 -
Num. residues----854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077108
X-RAY DIFFRACTIONf_angle_d1.1419586
X-RAY DIFFRACTIONf_chiral_restr0.0491031
X-RAY DIFFRACTIONf_plane_restr0.0061204
X-RAY DIFFRACTIONf_dihedral_angle_d12.2652599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2883X-RAY DIFFRACTION7.862TORSIONAL
12B2883X-RAY DIFFRACTION7.862TORSIONAL
13D2883X-RAY DIFFRACTION7.862TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.32351790.31273330350998
1.7193-1.73950.36291740.31643333350798
1.7395-1.76070.29971810.29893297347898
1.7607-1.7830.3571490.29373406355598
1.783-1.80650.31391850.27473383356898
1.8065-1.83120.29621950.26563319351499
1.8312-1.85730.29721790.27413360353999
1.8573-1.8850.30251700.27663386355699
1.885-1.91450.3141730.25963399357299
1.9145-1.94580.26481530.23063392354599
1.9458-1.97930.24391700.22093407357799
1.9793-2.01530.2071860.20583383356999
2.0153-2.0540.22431780.192133793557100
2.054-2.09590.21021840.200734143598100
2.0959-2.14140.2331750.182334543629100
2.1414-2.19120.2251760.183833593535100
2.1912-2.24590.23991960.185833943590100
2.2459-2.30650.22811760.187134193595100
2.3065-2.37430.22051730.186834363609100
2.3743-2.45080.21381790.191834173596100
2.4508-2.53820.24511600.19534453605100
2.5382-2.63970.23971770.187334323609100
2.6397-2.75950.2231700.191134663636100
2.7595-2.90460.21021810.193434103591100
2.9046-3.08590.22531720.189234383610100
3.0859-3.32320.19691940.177134283622100
3.3232-3.65570.17721540.167834643618100
3.6557-4.18050.20591850.155434373622100
4.1805-5.25090.13571970.142834423639100
5.2509-19.90340.20091830.17663475365899
Refinement TLS params.Method: refined / Origin x: 25.7106 Å / Origin y: 4.9808 Å / Origin z: -17.6784 Å
111213212223313233
T0.121 Å20.0082 Å2-0.0026 Å2-0.1258 Å2-0.0153 Å2--0.1408 Å2
L0.1009 °20.0465 °2-0.0522 °2-0.0851 °2-0.0356 °2--0.2287 °2
S0.0079 Å °-0.0238 Å °-0.0034 Å °0.0046 Å °-0.0002 Å °-0.0016 Å °-0.0058 Å °0.036 Å °-0.0062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA45 - 264
2X-RAY DIFFRACTION1allB45 - 264
3X-RAY DIFFRACTION1allC45 - 265
4X-RAY DIFFRACTION1allD46 - 265
5X-RAY DIFFRACTION1allF1 - 8
6X-RAY DIFFRACTION1allF8
7X-RAY DIFFRACTION1allG1 - 8
8X-RAY DIFFRACTION1allG8
9X-RAY DIFFRACTION1allH1 - 8
10X-RAY DIFFRACTION1allH8
11X-RAY DIFFRACTION1allW1 - 797
12X-RAY DIFFRACTION1allI1 - 7
13X-RAY DIFFRACTION1allE1 - 7
14X-RAY DIFFRACTION1allE8

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