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- PDB-6vil: Crystal structure of mouse BAHCC1 BAH domain in complex with H3K27me3 -

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Basic information

Entry
Database: PDB / ID: 6vil
TitleCrystal structure of mouse BAHCC1 BAH domain in complex with H3K27me3
Components
  • BAH and coiled-coil domain-containing protein 1
  • Histone H3.1
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


Chromatin modifying enzymes / telomere organization / 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 / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) ...Chromatin modifying enzymes / telomere organization / 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 / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / locomotory behavior / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / neuron differentiation / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
: / : / TNRC18-like,(4.1.1) SH3 / : / : / BAHCC1-like, Tudor domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain ...: / : / TNRC18-like,(4.1.1) SH3 / : / : / BAHCC1-like, Tudor domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SH3 type barrels. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / BAH and coiled-coil domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsSong, J. / Lu, J.
CitationJournal: Nat.Genet. / Year: 2020
Title: BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis.
Authors: Fan, H. / Lu, J. / Guo, Y. / Li, D. / Zhang, Z.M. / Tsai, Y.H. / Pi, W.C. / Ahn, J.H. / Gong, W. / Xiang, Y. / Allison, D.F. / Geng, H. / He, S. / Diao, Y. / Chen, W.Y. / Strahl, B.D. / Cai, ...Authors: Fan, H. / Lu, J. / Guo, Y. / Li, D. / Zhang, Z.M. / Tsai, Y.H. / Pi, W.C. / Ahn, J.H. / Gong, W. / Xiang, Y. / Allison, D.F. / Geng, H. / He, S. / Diao, Y. / Chen, W.Y. / Strahl, B.D. / Cai, L. / Song, J. / Wang, G.G.
History
DepositionJan 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.2Nov 11, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 18, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BAH and coiled-coil domain-containing protein 1
B: BAH and coiled-coil domain-containing protein 1
I: Histone H3.1
J: Histone H3.1
D: BAH and coiled-coil domain-containing protein 1
E: BAH and coiled-coil domain-containing protein 1
F: BAH and coiled-coil domain-containing protein 1
G: BAH and coiled-coil domain-containing protein 1
H: BAH and coiled-coil domain-containing protein 1
C: BAH and coiled-coil domain-containing protein 1
L: Histone H3.1
M: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)154,15612
Polymers154,15612
Non-polymers00
Water00
1
A: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,5391
Polymers18,5391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BAH and coiled-coil domain-containing protein 1
J: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Histone H3.1
C: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,5391
Polymers18,5391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: BAH and coiled-coil domain-containing protein 1
L: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,5391
Polymers18,5391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: BAH and coiled-coil domain-containing protein 1
M: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: BAH and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,5391
Polymers18,5391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.176, 184.176, 70.276
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
BAH and coiled-coil domain-containing protein 1


Mass: 18539.135 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bahcc1, Kiaa1447 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3UHR0
#2: Protein/peptide
Histone H3.1


Mass: 1460.699 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
Has ligand of interestY

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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: 4.46 Å3/Da / Density % sol: 72.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 1.6-1.8 M NaH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 40066 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.107 / Rrim(I) all: 0.218 / Χ2: 0.531 / Net I/σ(I): 3.2 / Num. measured all: 162176
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.4241.35439950.2970.7661.5590.501100
3.42-3.554.10.95440040.5120.5281.0920.497100
3.55-3.724.10.63640260.7530.3550.730.51199.5
3.72-3.914.10.40840080.8660.230.4690.509100
3.91-4.163.80.26939880.930.1590.3130.512100
4.16-4.483.90.15440300.9720.0890.1780.538100
4.48-4.934.20.13139980.9830.0720.150.528100
4.93-5.644.10.11839840.9850.0660.1350.532100
5.64-7.13.90.10440250.9870.0610.1210.545100
7.1-504.10.04740080.9980.0260.0540.634100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOV

4dov


Resolution: 3.301→46.044 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.33
RfactorNum. reflection% reflection
Rfree0.2828 2016 5.04 %
Rwork0.2479 --
obs0.2497 40020 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.08 Å2 / Biso mean: 93.7795 Å2 / Biso min: 41.3 Å2
Refinement stepCycle: final / Resolution: 3.301→46.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9381 0 0 0 9381
Num. residues----1245
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.301-3.38310.38891380.35132701100
3.3831-3.47450.37191560.32842741100
3.4745-3.57670.36341400.32352706100
3.5767-3.69210.34221420.30742703100
3.6921-3.8240.31141380.27632718100
3.824-3.9770.28091460.24722707100
3.977-4.15790.28641490.24032729100
4.1579-4.3770.24511490.21122744100
4.377-4.6510.28521440.20052698100
4.651-5.00970.25961400.2132719100
5.0097-5.51310.2611400.21842730100
5.5131-6.30910.31321480.24142696100
6.3091-7.94210.27371350.25932734100
7.9421-46.0440.22231510.2465267899
Refinement TLS params.Method: refined / Origin x: 48.9578 Å / Origin y: -21.0584 Å / Origin z: -11.1408 Å
111213212223313233
T0.3207 Å20.1868 Å2-0.0361 Å2-0.7006 Å20.0063 Å2--0.559 Å2
L0.6618 °2-0.2291 °2-0.3335 °2-0.3655 °20.0571 °2--1.691 °2
S0.0318 Å °0.1854 Å °-0.0143 Å °0.0597 Å °-0.0818 Å °-0.0149 Å °-0.2043 Å °0.1419 Å °0.0464 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2486 - 2642
2X-RAY DIFFRACTION1allB2486 - 2641
3X-RAY DIFFRACTION1allI22 - 33
4X-RAY DIFFRACTION1allJ22 - 33
5X-RAY DIFFRACTION1allD2485 - 2642
6X-RAY DIFFRACTION1allE2485 - 2642
7X-RAY DIFFRACTION1allF2487 - 2642
8X-RAY DIFFRACTION1allG2485 - 2642
9X-RAY DIFFRACTION1allH2485 - 2642
10X-RAY DIFFRACTION1allC2485 - 2642
11X-RAY DIFFRACTION1allL25 - 29
12X-RAY DIFFRACTION1allM25 - 28

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