[English] 日本語
Yorodumi
- PDB-7ubo: Crystal Structure of the first bromodomain of human BRDT in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ubo
TitleCrystal Structure of the first bromodomain of human BRDT in complex with the inhibitor CCD-956
ComponentsBromodomain testis-specific protein
KeywordsTRANSCRIPTION/INHIBITOR / INHIBITOR / REGULATOR / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone H4 reader activity / : / RNA splicing / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone H4 reader activity / : / RNA splicing / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MJN / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTa, H.M. / Modukuri, R.K. / Yu, Z. / Tan, Z. / Matzuk, M.M. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)P01HD087157 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Discovery of potent BET bromodomain 1 stereoselective inhibitors using DNA-encoded chemical library selections.
Authors: Modukuri, R.K. / Yu, Z. / Tan, Z. / Ta, H.M. / Ucisik, M.N. / Jin, Z. / Anglin, J.L. / Sharma, K.L. / Nyshadham, P. / Li, F. / Riehle, K. / Faver, J.C. / Duong, K. / Nagarajan, S. / Simmons, ...Authors: Modukuri, R.K. / Yu, Z. / Tan, Z. / Ta, H.M. / Ucisik, M.N. / Jin, Z. / Anglin, J.L. / Sharma, K.L. / Nyshadham, P. / Li, F. / Riehle, K. / Faver, J.C. / Duong, K. / Nagarajan, S. / Simmons, N. / Palmer, S.S. / Teng, M. / Young, D.W. / Yi, J.S. / Kim, C. / Matzuk, M.M.
History
DepositionMar 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromodomain testis-specific protein
B: Bromodomain testis-specific protein
C: Bromodomain testis-specific protein
D: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9269
Polymers52,5854
Non-polymers2,3415
Water8,593477
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7122
Polymers13,1461
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7903
Polymers13,1461
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7122
Polymers13,1461
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7122
Polymers13,1461
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.691, 94.382, 112.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 13146.237 Da / Num. of mol.: 4 / Fragment: first bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1_Alpha_S (others)
References: UniProt: Q58F21
#2: Chemical
ChemComp-MJN / N-[(2R)-1-(methylamino)-3-{1-[(4-methyl-2-oxo-1,2-dihydroquinolin-6-yl)acetyl]piperidin-4-yl}-1-oxopropan-2-yl]-5-phenylpyridine-2-carboxamide


Mass: 565.662 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H35N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.26 M Ammonium Sulfate, 0.1 M Tris 8.5, 0.2 M Lithium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→48.37 Å / Num. obs: 113916 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 8.3
Reflection shellResolution: 1.82→1.885 Å / Num. unique obs: 5882 / CC1/2: 0.306 / CC star: 0.684

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FLP

4flp


Resolution: 1.82→48.37 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 3820 3.35 %
Rwork0.1772 110096 -
obs0.1779 113916 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.28 Å2 / Biso mean: 34.0164 Å2 / Biso min: 16.29 Å2
Refinement stepCycle: final / Resolution: 1.82→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 178 477 4209
Biso mean--30.97 41.15 -
Num. residues----434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.82-1.840.3721390.348440264165
1.84-1.870.31081460.333441384284
1.87-1.890.32591390.306840204159
1.89-1.920.32091460.302241714317
1.92-1.950.29951400.27839954135
1.95-1.980.27531460.263841334279
1.98-2.010.24451440.243540564200
2.01-2.050.25761410.228940794220
2.05-2.080.23971420.218740664208
2.08-2.120.20921440.193240954239
2.12-2.170.23221410.190140554196
2.17-2.210.23951450.188341104255
2.21-2.270.19961430.1940534196
2.27-2.320.22661420.186240384180
2.32-2.380.19951360.180341104246
2.38-2.450.21761400.174540904230
2.46-2.530.22151380.164740584196
2.53-2.620.1861420.172541314273
2.62-2.730.21851370.168740244161
2.73-2.850.18291450.176540904235
2.85-30.21691440.170940914235
3-3.190.23411420.172940804222
3.19-3.440.18121350.157840834218
3.44-3.780.14631410.14340804221
3.79-4.330.15421390.131240814220
4.33-5.460.15361470.142640664213
5.46-48.370.16941360.165640774213
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)
19.00965.12834.98893.47434.3487.85540.22220.2405-0.78090.13180.1271-0.68810.47740.545-0.32570.21370.03410.00780.24960.0260.258212.64-32.78412.085
26.9633-6.7304-5.69299.36127.13315.6887-0.039-0.07930.4914-0.07270.4252-0.4965-0.24630.758-0.31470.2175-0.0195-0.00540.24710.02760.19389.152-24.62119.718
37.14224.2117-3.55635.7977-3.03613.67850.1312-0.51740.03180.537-0.13740.2212-0.17960.09760.03650.24270.02040.02830.192-0.00820.1612-4.066-26.2830.497
46.26390.2005-5.69955.4352-1.87228.9804-0.06640.1831-0.4073-0.0099-0.00110.31560.0745-0.35590.16460.2066-0.00830.01860.17760.02280.2753-8.738-35.92225.369
53.9368-1.0218-5.86745.32463.03479.1866-0.4032-0.5449-0.790.6897-0.0062-0.11420.55630.60940.3050.22530.0190.02250.21110.09710.3027.203-35.41723.2
62.6565-2.66951.70976.1364-4.94584.14190.2420.6322-0.7856-0.5681-0.4617-0.18370.2490.41530.12320.33360.07150.0310.216-0.01130.29418.031-41.80416.413
73.7292-0.9365-4.03920.26221.04964.5345-0.19280.1533-0.5846-0.03930.04460.36520.2143-0.09240.19950.1954-0.0073-0.00470.14370.00590.2686-4.151-31.87517.181
86.05644.86296.00124.83675.42456.3402-0.157-0.92260.55680.2732-0.1052.6259-0.5512-0.66710.36550.2640.03060.01590.2831-0.00340.4911-14.701-21.16823.973
95.1975-3.8502-5.48462.75714.07215.1420.0980.41540.1391-0.0669-0.1746-0.0265-0.1382-0.3469-0.04570.2401-0.0007-0.01280.23620.00830.26150.86-22.98813.413
103.4636-0.0737-1.0932.57090.82767.1314-0.1126-1.4191-0.28681.1240.0967-0.9940.57820.6610.02410.39150.0717-0.1320.3426-0.00490.320418.284-8.76637.178
113.3158-4.3391.46125.8565-2.56482.9659-0.5445-0.58750.51650.62650.3273-0.1808-0.20420.0980.17520.32910.01410.02270.2426-0.05590.21649.332-1.4135.451
124.40941.74521.96936.31392.10133.87090.1893-0.09450.116-0.067-0.25090.5676-0.0249-0.39020.07380.19210.03550.03310.1974-0.00510.2527-3.152-3.49824.117
135.7971-1.08815.04414.8339-2.4696.7840.1351-0.1123-0.22070.1756-0.0599-0.04090.45250.053-0.15490.22550.01110.03990.152-0.00380.16666.737-13.35926.471
147.6157-2.27226.05631.2113-2.08785.02840.20690.0286-0.036-0.0688-0.0351-0.06130.21370.1982-0.18410.26570.0210.02960.1991-0.03570.20510.575-6.97321.4
154.4738-1.65320.25532.57021.48932.11620.55080.65930.8584-1.7122-0.34380.3743-0.7304-0.345-0.04330.41890.05980.04290.26510.03720.35161.0283.64613.205
163.7211-2.40474.38064.2938-1.5826.89090.025-0.23570.3570.20830.0673-0.4938-0.10180.4414-0.00510.21840.00430.03210.2093-0.05990.240913.7011.89426.796
173.263-1.38680.46214.7943-2.12724.153-0.04990.4040.034-0.30260.13490.0926-0.0776-0.1419-0.10610.1562-0.0517-0.00350.2696-0.01660.134816.238-17.357-2.876
185.5286-2.83920.78443.835-0.50191.2737-0.0412-0.02770.030.06450.17780.1151-0.1495-0.0545-0.12290.2091-0.03320.03560.2470.02030.149413.779-14.9155.363
195.5357-3.4786-1.27495.7850.66341.5550.1071-0.02760.3284-0.37070.0707-0.2996-0.18470.1058-0.14380.2292-0.05120.03710.3131-0.02090.170924.686-12.086-1.539
207.13641.31813.19445.49773.17312.791-0.16240.3740.6373-0.62640.18030.1776-1.4781-0.14280.05820.4311-0.00120.08060.24070.02180.403922.4859.0176.191
214.0498-0.7792-0.00731.8159-2.45773.92990.1112-0.09960.35450.2079-0.0363-0.65740.11170.8318-0.08440.2675-0.0304-0.05280.4208-0.19240.452334.292-2.83519.346
226.6922-3.586-1.25393.4616-1.0773.5622-0.07120.05870.6191-0.35320.3202-1.8075-0.02830.8447-0.1280.2931-0.06140.070.4685-0.13030.609938.974-6.7099.634
235.26032.380.94388.3254-5.4865.09350.07490.6080.7846-0.89190.2864-0.3722-0.50920.8622-0.1790.5075-0.16160.20130.41860.01050.646532.8528.1043.683
245.1874-3.9843.82925.8696-2.71846.01540.1370.21350.5228-0.482-0.1227-0.5161-0.14590.59190.06980.2637-0.07930.09230.3222-0.06650.360329.351-4.3546.166
258.6352-5.5536-6.55124.52214.49875.0653-0.87510.1845-0.71240.59720.11830.04841.6028-0.26740.67120.3497-0.00520.06510.3242-0.05620.358328.856-14.53918.802
268.4658-5.79896.78929.1959-5.92767.87120.13140.24570.2275-0.2943-0.04750.0201-0.18860.1256-0.13370.191-0.01360.06310.2408-0.05030.250219.395-1.7589.486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:37 )A29 - 37
2X-RAY DIFFRACTION2( CHAIN A AND RESID 38:45 )A38 - 45
3X-RAY DIFFRACTION3( CHAIN A AND RESID 46:65 )A46 - 65
4X-RAY DIFFRACTION4( CHAIN A AND RESID 66:75 )A66 - 75
5X-RAY DIFFRACTION5( CHAIN A AND RESID 76:84 )A76 - 84
6X-RAY DIFFRACTION6( CHAIN A AND RESID 85:90 )A85 - 90
7X-RAY DIFFRACTION7( CHAIN A AND RESID 91:108 )A91 - 108
8X-RAY DIFFRACTION8( CHAIN A AND RESID 109:113 )A109 - 113
9X-RAY DIFFRACTION9( CHAIN A AND RESID 114:136 )A114 - 136
10X-RAY DIFFRACTION10( CHAIN B AND RESID 29:37 )B29 - 37
11X-RAY DIFFRACTION11( CHAIN B AND RESID 38:45 )B38 - 45
12X-RAY DIFFRACTION12( CHAIN B AND RESID 46:65 )B46 - 65
13X-RAY DIFFRACTION13( CHAIN B AND RESID 66:90 )B66 - 90
14X-RAY DIFFRACTION14( CHAIN B AND RESID 91:108 )B91 - 108
15X-RAY DIFFRACTION15( CHAIN B AND RESID 109:113 )B109 - 113
16X-RAY DIFFRACTION16( CHAIN B AND RESID 114:136 )B114 - 136
17X-RAY DIFFRACTION17( CHAIN C AND RESID 28:65 )C28 - 65
18X-RAY DIFFRACTION18( CHAIN C AND RESID 66:108 )C66 - 108
19X-RAY DIFFRACTION19( CHAIN C AND RESID 109:135 )C109 - 135
20X-RAY DIFFRACTION20( CHAIN D AND RESID 29:45 )D29 - 45
21X-RAY DIFFRACTION21( CHAIN D AND RESID 46:65 )D46 - 65
22X-RAY DIFFRACTION22( CHAIN D AND RESID 66:75 )D66 - 75
23X-RAY DIFFRACTION23( CHAIN D AND RESID 76:90 )D76 - 90
24X-RAY DIFFRACTION24( CHAIN D AND RESID 91:108 )D91 - 108
25X-RAY DIFFRACTION25( CHAIN D AND RESID 109:113 )D109 - 113
26X-RAY DIFFRACTION26( CHAIN D AND RESID 114:136 )D114 - 136

+
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