[English] 日本語
Yorodumi
- PDB-4qy4: Crystal structure of the bromodomain of human SMARCA2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qy4
TitleCrystal structure of the bromodomain of human SMARCA2
ComponentsSMARCA2 protein
KeywordsUNKNOWN FUNCTION / SMARCA2 BAF190B BRM SNF2A SNF2L2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


bBAF complex / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / ATP-dependent chromatin remodeler activity / SWI/SNF complex ...bBAF complex / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / ATP-dependent chromatin remodeler activity / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / intermediate filament cytoskeleton / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / spermatid development / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / helicase activity / positive regulation of cell differentiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of cell growth / RMTs methylate histone arginines / nervous system development / histone binding / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
SWI/SNF complex subunit SMARCA2 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ ...SWI/SNF complex subunit SMARCA2 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Probable global transcription activator SNF2L2 / cDNA FLJ36757 fis, clone UTERU2018522, highly similar to Human transcriptional activator hSNF2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsTallant, C. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Tallant, C. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the bromodomain of human SMARCA2
Authors: Tallant, C. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: SMARCA2 protein
B: SMARCA2 protein
C: SMARCA2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3386
Polymers43,1423
Non-polymers1963
Water1,76598
1
A: SMARCA2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4462
Polymers14,3811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SMARCA2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4462
Polymers14,3811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SMARCA2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4462
Polymers14,3811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.346, 64.346, 89.117
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein SMARCA2 protein


Mass: 14380.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q8N9Q1, UniProt: P51531*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG 6K, 8% ethylene glycol, 0.01M ZnCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.97→55.73 Å / Num. all: 28970 / Num. obs: 28970 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 18.046 Å2 / Rmerge(I) obs: 0.219 / Rsym value: 0.141 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value
1.99-2.0463.292.8103551.324
2.04-2.16.42.3973.8130990.934
2.1-2.156.81.7474.9133090.663
2.15-2.226.71.1016127440.421
2.22-2.296.20.7417.1114240.294
2.29-2.376.70.5388.1121340.205
2.37-2.456.50.4169.1111460.162
2.45-2.556.50.3710.399440.144
2.55-2.666.20.33311.399000.133
2.66-2.786.50.29312.998280.115
7.36-12.746.90.13425.338470.05

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY.

2grc

2oss

3d7c

2ouo

2oo1

3dai

3dwy


Resolution: 1.97→55.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / SU B: 9.877 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.183 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27889 1415 4.9 %RANDOM
Rwork0.22367 ---
all0.22633 28970 --
obs0.22633 27508 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å2-0 Å2
3----2.36 Å2
Refinement stepCycle: LAST / Resolution: 1.97→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 3 98 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192690
X-RAY DIFFRACTIONr_bond_other_d0.0010.022680
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9763607
X-RAY DIFFRACTIONr_angle_other_deg0.8436171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00824.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29715547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8891520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
X-RAY DIFFRACTIONr_mcbond_it1.4731.8271289
X-RAY DIFFRACTIONr_mcbond_other1.4721.8251288
X-RAY DIFFRACTIONr_mcangle_it2.2622.7251606
X-RAY DIFFRACTIONr_mcangle_other2.2622.7271607
X-RAY DIFFRACTIONr_scbond_it1.9412.081401
X-RAY DIFFRACTIONr_scbond_other1.942.0821402
X-RAY DIFFRACTIONr_scangle_other3.1623.0162002
X-RAY DIFFRACTIONr_long_range_B_refined5.05414.5233177
X-RAY DIFFRACTIONr_long_range_B_other5.0114.4123155
LS refinement shellResolution: 1.968→2.019 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 111 -
Rwork0.326 1758 -
obs--85.85 %
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)
10.4344-0.1047-0.02560.85720.05531.9281-0.00560.1666-0.03470.0862-0.0463-0.124-0.1494-0.10860.05190.11640.05430.03490.13370.03970.107528.047420.407618.473
20.5123-0.13680.04830.39120.23571.62020.02260.0113-0.02130.0465-0.07590.00970.0061-0.15930.05320.13070.06460.04810.1541-0.01030.08741.80034.433726.213
30.96230.99180.32761.3861.17292.089-0.01560.43230.17590.28020.5225-0.04060.52070.3587-0.5070.16810.1634-0.1360.4316-0.01130.16772.738831.58083.6272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1381 - 1490
2X-RAY DIFFRACTION2B1383 - 1490
3X-RAY DIFFRACTION3C1383 - 1487

+
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://pdbjlvh1.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