[English] 日本語
Yorodumi
- PDB-8pyr: Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat... -

+
Open data


ID or keywords:

Loading...

-
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


RNA polymerase II CTD heptapeptide repeat S5 kinase activity / ventricular system development / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / [RNA-polymerase]-subunit kinase ...RNA polymerase II CTD heptapeptide repeat S5 kinase activity / ventricular system development / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / [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 / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / RNA Polymerase I Transcription Initiation / regulation of G1/S transition of mitotic cell cycle / RNA polymerase II transcribes snRNA genes / ATP-dependent activity, acting on DNA / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of smooth muscle cell proliferation / RNA polymerase II CTD heptapeptide repeat kinase activity / male germ cell nucleus / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / G1/S transition of mitotic cell cycle / response to calcium ion / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / fibrillar center / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / kinase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription by RNA polymerase II / protein kinase activity / regulation of cell cycle / protein stabilization / 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
Citation
Journal: Nat Commun / 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.
#1: Journal: 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
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 30, 2025Group: Database references / Category: citation / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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)

-
Non-polymers , 2 types, 390 molecules

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


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


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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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