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- PDB-9mxk: BRD4-BD1 in complex with cyclic peptide 4.1C -

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Basic information

Entry
Database: PDB / ID: 9mxk
TitleBRD4-BD1 in complex with cyclic peptide 4.1C
Components
  • 4.1C
  • Bromodomain-containing protein 4
KeywordsGENE REGULATION / BRD4 / cyclic peptide
Function / homology
Function and homology information


histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / histone H3K9ac reader activity / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription ...histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / histone H3K9ac reader activity / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / 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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPatel, K. / Pachl, P. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: BRD4-BD1 in complex with cyclic peptide 4.1C
Authors: Patel, K. / Mackay, J.P.
History
DepositionJan 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: 4.1C
D: Bromodomain-containing protein 4
E: 4.1C
I: Bromodomain-containing protein 4
J: 4.1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,43010
Polymers53,4776
Non-polymers9534
Water2,540141
1
A: Bromodomain-containing protein 4
B: 4.1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0643
Polymers17,8262
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area7610 Å2
MethodPISA
2
D: Bromodomain-containing protein 4
E: 4.1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0643
Polymers17,8262
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-12 kcal/mol
Surface area7600 Å2
MethodPISA
3
I: Bromodomain-containing protein 4
J: 4.1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3024
Polymers17,8262
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-12 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.121, 70.121, 90.16
Angle α, β, γ (deg.)90, 90, 120
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21D
32A
42I
53B
63E
74B
84J
95D
105I
116E
126J

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERTHRTHRAA41 - 1666 - 131
211SERSERTHRTHRDC41 - 1666 - 131
322SERSERTHRTHRAA41 - 1666 - 131
422SERSERTHRTHRIE41 - 1666 - 131
533ACEACENH2NH2BB0 - 171 - 18
633ACEACENH2NH2ED0 - 171 - 18
744ACEACENH2NH2BB0 - 171 - 18
844ACEACENH2NH2JF0 - 171 - 18
955SERSERPROPRODC41 - 1656 - 130
1055SERSERPROPROIE41 - 1656 - 130
1166ACEACENH2NH2ED0 - 171 - 18
1266ACEACENH2NH2JF0 - 171 - 18

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15608.872 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Protein/peptide 4.1C


Mass: 2216.716 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 42% v/v Polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.6
pseudo-merohedral22K, H, -L20.4
ReflectionResolution: 1.73→19.751 Å / Num. obs: 45685 / % possible obs: 94.6 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rrim(I) all: 0.147 / Net I/σ(I): 7.5
Reflection shell

Num. unique obs: 2284 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Rrim(I) all% possible all
4.874-19.7517.519.90.9990.053100
1.73-1.8327.21.30.2421.36747.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→19.751 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.157 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.023
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2129 2051 4.49 %
Rwork0.1757 43633 -
all0.177 --
obs-45684 88.162 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.237 Å2
Baniso -1Baniso -2Baniso -3
1--0.271 Å2-0 Å2-0 Å2
2---0.271 Å2-0 Å2
3---0.542 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 64 141 3504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123449
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163233
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.8184663
X-RAY DIFFRACTIONr_angle_other_deg0.6571.7487490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.55459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82810559
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.03610151
X-RAY DIFFRACTIONr_chiral_restr0.1010.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02770
X-RAY DIFFRACTIONr_nbd_refined0.2120.2741
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.23037
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21697
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1820.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3560.29
X-RAY DIFFRACTIONr_nbd_other0.2260.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.25
X-RAY DIFFRACTIONr_mcbond_it3.8542.8141616
X-RAY DIFFRACTIONr_mcbond_other3.8432.8141615
X-RAY DIFFRACTIONr_mcangle_it4.6595.0672005
X-RAY DIFFRACTIONr_mcangle_other4.6585.0662005
X-RAY DIFFRACTIONr_scbond_it4.3863.0111833
X-RAY DIFFRACTIONr_scbond_other4.3853.0111834
X-RAY DIFFRACTIONr_scangle_it5.5725.4762658
X-RAY DIFFRACTIONr_scangle_other5.5715.4752659
X-RAY DIFFRACTIONr_lrange_it6.40928.5083857
X-RAY DIFFRACTIONr_lrange_other6.4128.5043844
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.053771
X-RAY DIFFRACTIONr_ncsr_local_group_20.0780.053746
X-RAY DIFFRACTIONr_ncsr_local_group_30.0760.05497
X-RAY DIFFRACTIONr_ncsr_local_group_40.1040.05500
X-RAY DIFFRACTIONr_ncsr_local_group_50.0830.053736
X-RAY DIFFRACTIONr_ncsr_local_group_60.0980.05496
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.08890.05007
12DX-RAY DIFFRACTIONLocal ncs0.08890.05007
23AX-RAY DIFFRACTIONLocal ncs0.077960.05007
24IX-RAY DIFFRACTIONLocal ncs0.077960.05007
35BX-RAY DIFFRACTIONLocal ncs0.075810.05007
36EX-RAY DIFFRACTIONLocal ncs0.075810.05007
47BX-RAY DIFFRACTIONLocal ncs0.104290.05007
48JX-RAY DIFFRACTIONLocal ncs0.104290.05007
59DX-RAY DIFFRACTIONLocal ncs0.083330.05007
510IX-RAY DIFFRACTIONLocal ncs0.083330.05007
611EX-RAY DIFFRACTIONLocal ncs0.097840.05007
612JX-RAY DIFFRACTIONLocal ncs0.097840.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.7740.253140.247233X-RAY DIFFRACTION6.4508
1.774-1.8230.272710.2111496X-RAY DIFFRACTION41.8648
1.823-1.8760.2371330.1983180X-RAY DIFFRACTION90.6678
1.876-1.9340.2511920.1853314X-RAY DIFFRACTION100
1.934-1.9970.241900.1943244X-RAY DIFFRACTION100
1.997-2.0670.2291680.1853133X-RAY DIFFRACTION100
2.067-2.1450.2131760.1712995X-RAY DIFFRACTION100
2.145-2.2330.2071110.1762974X-RAY DIFFRACTION100
2.233-2.3320.2131020.1832894X-RAY DIFFRACTION100
2.332-2.4450.2371340.182637X-RAY DIFFRACTION100
2.445-2.5780.231820.182597X-RAY DIFFRACTION100
2.578-2.7340.244620.1892451X-RAY DIFFRACTION100
2.734-2.9220.1951150.1852304X-RAY DIFFRACTION100
2.922-3.1560.2281170.1682081X-RAY DIFFRACTION100
3.156-3.4570.1831140.1591920X-RAY DIFFRACTION100
3.457-3.8640.19580.1611794X-RAY DIFFRACTION100
3.864-4.4610.167880.1581519X-RAY DIFFRACTION100
4.461-5.460.221580.1731326X-RAY DIFFRACTION100
5.46-7.7080.203380.1981018X-RAY DIFFRACTION100
7.708-19.7510.387280.18523X-RAY DIFFRACTION94.0273

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