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- PDB-8pyr: Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat... -

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Basic information

Entry
Database: PDB / ID: 8pyr
TitleCrystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex
Components
  • CDK-activating kinase assembly factor MAT1
  • Cyclin-H
  • Cyclin-dependent kinase 7
  • Nanobody (VHH-RD7-04)
KeywordsTRANSCRIPTION / Cdk7 / Cyclin H / Mat1 / CDK activating kinase / kinase / phosphorylation
Function / homology
Function and homology information


negative regulation of DNA helicase activity / ventricular system development / cyclin-dependent protein kinase activating kinase holoenzyme complex / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex ...negative regulation of DNA helicase activity / ventricular system development / cyclin-dependent protein kinase activating kinase holoenzyme complex / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / [RNA-polymerase]-subunit kinase / RNA Polymerase I Transcription Termination / cyclin-dependent protein serine/threonine kinase regulator activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ATP-dependent activity, acting on DNA / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / Cyclin E associated events during G1/S transition / RNA Polymerase II Transcription Elongation / Cyclin A/B1/B2 associated events during G2/M transition / Formation of RNA Pol II elongation complex / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of smooth muscle cell proliferation / NoRC negatively regulates rRNA expression / G1/S transition of mitotic cell cycle / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / Formation of Incision Complex in GG-NER / response to calcium ion / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / protein-containing complex assembly / transcription by RNA polymerase II / protein stabilization / regulation of cell cycle / protein kinase activity / cell cycle / phosphorylation / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Ubiquitin interacting motif ...CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Cyclin-dependent kinase 7 / Cyclin-H / CDK-activating kinase assembly factor MAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsAnand, K. / Duster, R. / Geyer, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC2151-390873048 Germany
CitationJournal: Biorxiv / Year: 2024
Title: Structural basis of Cdk7 activation by dual T-loop phosphorylation.
Authors: Duster, R. / Anand, K. / Binder, S.C. / Schmitz, M. / Gatterdam, K. / Fisher, R.P. / Geyer, M.
History
DepositionJul 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 7
B: Cyclin-H
C: CDK-activating kinase assembly factor MAT1
D: Nanobody (VHH-RD7-04)
E: Cyclin-dependent kinase 7
F: Cyclin-H
G: CDK-activating kinase assembly factor MAT1
H: Nanobody (VHH-RD7-04)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,23814
Polymers196,8668
Non-polymers3726
Water6,918384
1
A: Cyclin-dependent kinase 7
B: Cyclin-H
C: CDK-activating kinase assembly factor MAT1
D: Nanobody (VHH-RD7-04)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6197
Polymers98,4334
Non-polymers1863
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-43 kcal/mol
Surface area29750 Å2
MethodPISA
2
E: Cyclin-dependent kinase 7
F: Cyclin-H
G: CDK-activating kinase assembly factor MAT1
H: Nanobody (VHH-RD7-04)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6197
Polymers98,4334
Non-polymers1863
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-41 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.860, 77.866, 121.872
Angle α, β, γ (deg.)90.00, 119.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules AEBFCG

#1: Protein Cyclin-dependent kinase 7 / / 39 kDa protein kinase / p39 Mo15 / CDK-activating kinase 1 / Cell division protein kinase 7 / ...39 kDa protein kinase / p39 Mo15 / CDK-activating kinase 1 / Cell division protein kinase 7 / Serine/threonine-protein kinase 1 / TFIIH basal transcription factor complex kinase subunit


Mass: 39250.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK7, CAK, CAK1, CDKN7, MO15, STK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P50613, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-H / MO15-associated protein / p34 / p37


Mass: 37695.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51946
#3: Protein CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36


Mass: 9043.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51948

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Antibody , 1 types, 2 molecules DH

#4: Antibody Nanobody (VHH-RD7-04)


Mass: 12443.868 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 2 types, 390 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→48.05 Å / Num. obs: 106560 / % possible obs: 98.97 % / Redundancy: 10.2 % / CC1/2: 0.998 / Net I/σ(I): 7.79
Reflection shellResolution: 2.15→2.227 Å / Num. unique obs: 9834 / CC1/2: 0.325

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.05 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 62.7 / Phase error: 32.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2415 2041 1.93 %
Rwork0.2197 --
obs0.2226 105608 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11616 0 24 384 12024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211916
X-RAY DIFFRACTIONf_angle_d0.5716142
X-RAY DIFFRACTIONf_dihedral_angle_d13.5174436
X-RAY DIFFRACTIONf_chiral_restr0.0421779
X-RAY DIFFRACTIONf_plane_restr0.0042075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.34361390.34366716X-RAY DIFFRACTION89
2.2-2.260.35461370.35467271X-RAY DIFFRACTION95
2.26-2.330.37131430.34247325X-RAY DIFFRACTION97
2.33-2.410.3371380.33027407X-RAY DIFFRACTION98
2.41-2.490.31751510.31317431X-RAY DIFFRACTION98
2.49-2.590.31361390.29277431X-RAY DIFFRACTION98
2.59-2.710.31551390.27497445X-RAY DIFFRACTION98
2.71-2.850.31491450.27087438X-RAY DIFFRACTION98
2.85-3.030.28061440.25347459X-RAY DIFFRACTION98
3.03-3.260.28241380.25167468X-RAY DIFFRACTION98
3.26-3.590.23161550.22637503X-RAY DIFFRACTION98
3.59-4.110.21621430.19157494X-RAY DIFFRACTION98
4.11-5.180.19121510.16967532X-RAY DIFFRACTION98
5.18-100.20261520.17527674X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -7.4108 Å / Origin y: 16.5688 Å / Origin z: 70.8206 Å
111213212223313233
T0.3108 Å20.0065 Å2-0.1295 Å2-0.2805 Å2-0.0329 Å2--0.6362 Å2
L0.2561 °2-0.019 °2-0.2069 °2-0.2006 °20.0067 °2--0.5568 °2
S-0.0166 Å °0.0086 Å °-0.0113 Å °0.0436 Å °0.0006 Å °-0.1228 Å °-0.0219 Å °0.0129 Å °0.015 Å °
Refinement TLS groupSelection details: all

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