[English] 日本語
Yorodumi
- PDB-9qkz: Cryo-EM structure of CDK11B-cyclin L2-SAP30BP bound to AMP-PNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qkz
TitleCryo-EM structure of CDK11B-cyclin L2-SAP30BP bound to AMP-PNP
Components
  • Cyclin-L2
  • Cyclin-dependent kinase 11B
  • SAP30-binding protein
KeywordsSPLICING / kinase / cyclin-dependent kinase / transcription / molecular complex
Function / homology
Function and homology information


mitotic sister chromatid cohesion, centromeric / regulation of mRNA processing / regulation of centrosome cycle / intermediate filament cytoskeleton / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of RNA splicing / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex ...mitotic sister chromatid cohesion, centromeric / regulation of mRNA processing / regulation of centrosome cycle / intermediate filament cytoskeleton / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of RNA splicing / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / Recruitment of mitotic centrosome proteins and complexes / regulation of cell growth / NoRC negatively regulates rRNA expression / response to virus / mitotic cell cycle / regulation of apoptotic process / protein phosphorylation / protein kinase activity / regulation of cell cycle / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
SAP30-binding protein / HCNGP-like protein / Cyclin-dependent kinase 11/PITSLRE, catalytic domain / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like ...SAP30-binding protein / HCNGP-like protein / Cyclin-dependent kinase 11/PITSLRE, catalytic domain / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cyclin-dependent kinase 11B / Cyclin-L2 / SAP30-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsMcGeoch, A.J.S. / Cushing, V.I. / Cronin, N.B. / Alfieri, C. / Greber, B.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structures of the CDK11-cyclin L-SAP30BP complex reveal mechanisms of CDK11 regulation
Authors: McGeoch, A.J.S. / Cushing, V.I. / Roumeliotis, T.I. / Cronin, N.B. / Alfieri, C. / Greber, B.J. / Choudhary, J.
History
DepositionMar 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SAP30-binding protein
B: Cyclin-dependent kinase 11B
C: Cyclin-L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4826
Polymers119,9283
Non-polymers5553
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein SAP30-binding protein / Transcriptional regulator protein HCNGP


Mass: 34186.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAP30BP, HCNGP, HTRG, HTRP / Cell line (production host): High5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UHR5
#2: Protein Cyclin-dependent kinase 11B / Cell division cycle 2-like protein kinase 1 / CLK-1 / Cell division protein kinase 11B / ...Cell division cycle 2-like protein kinase 1 / CLK-1 / Cell division protein kinase 11B / Galactosyltransferase-associated protein kinase p58/GTA / PITSLRE serine/threonine-protein kinase CDC2L1 / p58 CLK-1


Mass: 50050.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK11B, CDC2L1, CDK11, PITSLREA, PK58 / Cell line (production host): High5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P21127, cyclin-dependent kinase
#3: Protein Cyclin-L2 / Paneth cell-enhanced expression protein


Mass: 35690.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNL2, SB138 / Cell line (production host): High5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96S94

-
Non-polymers , 3 types, 48 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: CDK11B-cyclin L2-SAP30BP-AMP-PNP complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
140 mMHEPES-KOH1
2200 mMPotassium chlorideKCl1
32 mMMagnesium chlorideMgCl21
45 mMbeta-mercaptoethanol1
51 mMAMP-PNP1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 36332
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPUimage acquisition
4cryoSPARC4.4.1CTF correction
5RELION5.0-betaCTF correction
8UCSF ChimeraXmodel fitting
10RELION5.0-betainitial Euler assignment
11RELION5.0-betafinal Euler assignment
12RELION5.0-betaclassification
13RELION5.0-beta3D reconstruction
14PHENIX1.21rc1_4985model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 783863 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035696
ELECTRON MICROSCOPYf_angle_d0.4647697
ELECTRON MICROSCOPYf_dihedral_angle_d4.978749
ELECTRON MICROSCOPYf_chiral_restr0.039839
ELECTRON MICROSCOPYf_plane_restr0.004975

+
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