[English] 日本語
Yorodumi
- PDB-3q2e: Crystal structure of the second bromodomain of human bromodomain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q2e
TitleCrystal structure of the second bromodomain of human bromodomain and WD repeat-containing protein 1 isoform A (WDR9)
ComponentsBromodomain and WD repeat-containing protein 1
KeywordsSIGNALING PROTEIN / Structural Genomics Consortium / SGC / Bromodomain / cell cycle progression / signal transduction / apoptosis / gene regulation / Down syndrome region-2 on chromosome 21
Function / homology
Function and homology information


motile cilium / ciliary membrane / axoneme / Chromatin modifying enzymes / cytoskeleton organization / Interleukin-7 signaling / regulation of cell shape / regulation of transcription by RNA polymerase II / nucleolus / nucleoplasm ...motile cilium / ciliary membrane / axoneme / Chromatin modifying enzymes / cytoskeleton organization / Interleukin-7 signaling / regulation of cell shape / regulation of transcription by RNA polymerase II / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / BRWD/PHIP ancillary domain-like domain / BRWD1-like, N-terminal domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain ...: / BRWD/PHIP ancillary domain-like domain / BRWD1-like, N-terminal domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Bromodomain and WD repeat-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsFilippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Krojer, T. / Muniz, J. / Gileadi, O. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Krojer, T. / Muniz, J. / Gileadi, O. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 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 / 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 / _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: Bromodomain and WD repeat-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5062
Polymers14,4471
Non-polymers591
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.660, 51.660, 151.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-90-

HOH

-
Components

#1: Protein Bromodomain and WD repeat-containing protein 1 / WD repeat-containing protein 9


Mass: 14447.411 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1310-1430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRWD1, C21orf107, WDR9 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9NSI6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.02 Å3/Da / Density % sol: 39.04 % / Mosaicity: 0.28 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M (NH4)COOCH3, 0.1M BisTris, 25% PEG 3350 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 5.6 / Number: 87081 / Rsym value: 0.088 / D res high: 1.74 Å / D res low: 28.892 Å / Num. obs: 12968 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.528.8997.910.0390.0395.6
3.895.510010.050.056
3.183.8910010.0670.0676.5
2.753.1810010.0610.0616.7
2.462.7510010.0810.0816.9
2.252.4699.810.1290.1297
2.082.2599.810.1850.1857
1.952.0899.610.3390.3397.1
1.831.9599.510.5410.5417.1
1.741.839810.870.876.1
ReflectionResolution: 1.74→28.892 Å / Num. all: 13033 / Num. obs: 12968 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.74-1.836.10.9510.870.91097317970.3750.9510.87298
1.83-1.957.10.5830.5411.41229017230.2160.5830.5413.899.5
1.95-2.087.10.3660.3392.21171216510.1360.3660.3395.899.6
2.08-2.2570.20.1854.11091315500.0750.20.1859.899.8
2.25-2.4670.1390.1295.7994214240.0520.1390.12913.299.8
2.46-2.756.90.0870.0818.9897713060.0330.0870.08117.5100
2.75-3.186.70.0660.06110.6789311710.0250.0660.06122100
3.18-3.896.50.0730.0677.9665810270.0290.0730.06726.4100
3.89-5.560.0540.0511.249418240.0220.0540.0528.9100
5.5-28.8925.60.0430.03914.127824950.0180.0430.0392997.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.93 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.46 Å
Translation2.5 Å25.46 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

3mb3

2oss

2ouo

2grc

2oo1

3dai

3d7c

3dwy


Resolution: 1.74→28.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2165 / WRfactor Rwork: 0.1822 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8744 / SU B: 4.247 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1125 / SU Rfree: 0.1098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 634 4.9 %RANDOM
Rwork0.1852 ---
all0.1867 13042 --
obs0.1867 12942 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.96 Å2 / Biso mean: 29.4449 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.74→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 4 105 971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022898
X-RAY DIFFRACTIONr_bond_other_d0.0020.02620
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9691217
X-RAY DIFFRACTIONr_angle_other_deg0.93431510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9155110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63524.56546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36315156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.969156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02186
X-RAY DIFFRACTIONr_mcbond_it2.9883547
X-RAY DIFFRACTIONr_mcbond_other0.9093211
X-RAY DIFFRACTIONr_mcangle_it4.6755887
X-RAY DIFFRACTIONr_scbond_it7.5938351
X-RAY DIFFRACTIONr_scangle_it10.53511328
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 47 -
Rwork0.348 845 -
all-892 -
obs--96.22 %
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)
1-4.54094.7643-5.668234.0038-1.003328.22970.0429-0.3715-0.2751-1.0918-0.2983-1.3835-0.3311.960.25540.04030.02430.07640.25430.05780.2233-5.509331.43310.7041
21.8641-1.21510.29470.8529-0.23850.70370.00910.0805-0.0695-0.0263-0.0475-0.0060.0107-0.03110.03840.1040.0118-0.00490.0503-0.0090.0545-26.217828.64463.9642
33.6206-0.6946-1.62740.6151-0.23121.27230.06160.06460.1289-0.0814-0.1019-0.1546-0.0553-0.05380.04040.13520.01720.01330.05040.02160.0744-19.469935.22693.326
43.5764-0.5475-0.54470.15690.02851.6515-0.1027-0.03710.19780.17080.1027-0.0884-0.22360.092400.150.0061-0.04090.0491-0.03420.0689-17.017532.681814.0421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1317 - 1323
2X-RAY DIFFRACTION2A1324 - 1362
3X-RAY DIFFRACTION3A1363 - 1395
4X-RAY DIFFRACTION4A1396 - 1423

+
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