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- EMDB-53224: Cryo-EM structure of CDK11B-cyclin L2-SAP30BP bound to AMP-PNP -

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Basic information

Entry
Database: EMDB / ID: EMD-53224
TitleCryo-EM structure of CDK11B-cyclin L2-SAP30BP bound to AMP-PNP
Map dataPost-processed cryo-EM map (sharpened, filtered)
Sample
  • Complex: CDK11B-cyclin L2-SAP30BP-AMP-PNP complex
    • Protein or peptide: SAP30-binding protein
    • Protein or peptide: Cyclin-dependent kinase 11B
    • Protein or peptide: Cyclin-L2
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordskinase / cyclin-dependent kinase / transcription / molecular complex / SPLICING
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
Cyclin-dependent kinase 11B / Cyclin-L2 / SAP30-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsMcGeoch AJS / Cushing VI / Cronin NB / Alfieri C / Greber BJ
Funding support United Kingdom, 1 items
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 AJS / Cushing VI / Roumeliotis TI / Cronin NB / Alfieri C / Greber BJ / Choudhary J
History
DepositionMar 20, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53224.png

Downloads & links

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Map

FileDownload / File: emd_53224.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed cryo-EM map (sharpened, filtered)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 192 pix.
= 193.536 Å		1.01 Å/pix.
x 192 pix.
= 193.536 Å		1.01 Å/pix.
x 192 pix.
= 193.536 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.008 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.06632098 - 0.15422471
Average (Standard dev.)0.000010880219 (±0.004185296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 193.53601 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53224_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Post-processed cryo-EM map (reduced sharpening, b = -10)

Fileemd_53224_additional_1.map
AnnotationPost-processed cryo-EM map (reduced sharpening, b = -10)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered cryo-EM half map from refinement

Fileemd_53224_half_map_1.map
AnnotationUnfiltered cryo-EM half map from refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered cryo-EM half map from refinement

Fileemd_53224_half_map_2.map
AnnotationUnfiltered cryo-EM half map from refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CDK11B-cyclin L2-SAP30BP-AMP-PNP complex

EntireName: CDK11B-cyclin L2-SAP30BP-AMP-PNP complex
Components
  • Complex: CDK11B-cyclin L2-SAP30BP-AMP-PNP complex
    • Protein or peptide: SAP30-binding protein
    • Protein or peptide: Cyclin-dependent kinase 11B
    • Protein or peptide: Cyclin-L2
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: CDK11B-cyclin L2-SAP30BP-AMP-PNP complex

SupramoleculeName: CDK11B-cyclin L2-SAP30BP-AMP-PNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: SAP30-binding protein

MacromoleculeName: SAP30-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.186633 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMAGKKNV LSSLAVYAED SEPESDGEAG IEAVGSAAEE KGGLVSDAYG EDDFSRLGGD EDGYEEEEDE NSRQSEDDDS ETEKPEADD PKDNTEAEKR DPQELVASFS ERVRNMSPDE IKIPPEPPGR CSNHLQDKIQ KLYERKIKEG MDMNYIIQRK K EFRNPSIY ...String:
SNAMAGKKNV LSSLAVYAED SEPESDGEAG IEAVGSAAEE KGGLVSDAYG EDDFSRLGGD EDGYEEEEDE NSRQSEDDDS ETEKPEADD PKDNTEAEKR DPQELVASFS ERVRNMSPDE IKIPPEPPGR CSNHLQDKIQ KLYERKIKEG MDMNYIIQRK K EFRNPSIY EKLIQFCAID ELGTNYPKDM FDPHGWSEDS YYEALAKAQK IEMDKLEKAK KERTKIEFVT GTKKGTTTNA TS TTTTTAS TAVADAQKRK SKWDSAIPVT TIAQPTILTT TATLPAVVTV TTSASGSKTT VISAVGTIVK KAKQ

UniProtKB: SAP30-binding protein

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Macromolecule #2: Cyclin-dependent kinase 11B

MacromoleculeName: Cyclin-dependent kinase 11B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.05059 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMSEDEER ENENHLLVVP ESRFDRDSGE SEEAEEEVGE GTPQSSALTE GDYVPDSPAL SPIELKQELP KYLPALQGCR SVEEFQCLN RIEEGTYGVV YRAKDKKTDE IVALKRLKME KEKEGFPITS LREINTILKA QHPNIVTVRE IVVGSNMDKI Y IVMNYVEH ...String:
SNAMSEDEER ENENHLLVVP ESRFDRDSGE SEEAEEEVGE GTPQSSALTE GDYVPDSPAL SPIELKQELP KYLPALQGCR SVEEFQCLN RIEEGTYGVV YRAKDKKTDE IVALKRLKME KEKEGFPITS LREINTILKA QHPNIVTVRE IVVGSNMDKI Y IVMNYVEH DLKSLMETMK QPFLPGEVKT LMIQLLRGVK HLHDNWILHR DLKTSNLLLS HAGILKVGDF GLAREYGSPL KA Y(TPO)PVVVT LWYRAPELLL GAKEYSTAVD MWSVGCIFGE LLTQKPLFPG KSEIDQINKV FKDLGTPSEK IWPGYSELP AVKKMTFSEH PYNNLRKRFG ALLSDQGFDL MNKFLTYFPG RRISAEDGLK HEYFRETPLP IDPSMFPTWP AKSEQQRVKR GT(SEP)PRPPEG GLGYSQLGDD DLKETGFHLT TTNQGASAAG PGFSLKF

UniProtKB: Cyclin-dependent kinase 11B

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Macromolecule #3: Cyclin-L2

MacromoleculeName: Cyclin-L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.690453 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMAAAAAA AGAAGSAAPA AAAGAPGSGG APSGSQGVLI GDRLYSGVLI TLENCLLPDD KLRFTPSMSS GLDTDTETDL RVVGCELIQ AAGILLRLPQ VAMATGQVLF QRFFYTKSFV KHSMEHVSMA CVHLASKIEE APRRIRDVIN VFHRLRQLRD K KKPVPLLL ...String:
SNAMAAAAAA AGAAGSAAPA AAAGAPGSGG APSGSQGVLI GDRLYSGVLI TLENCLLPDD KLRFTPSMSS GLDTDTETDL RVVGCELIQ AAGILLRLPQ VAMATGQVLF QRFFYTKSFV KHSMEHVSMA CVHLASKIEE APRRIRDVIN VFHRLRQLRD K KKPVPLLL DQDYVNLKNQ IIKAERRVLK ELGFCVHVKH PHKIIVMYLQ VLECERNQHL VQTSWNYMND SLRTDVFVRF QP ESIACAC IYLAARTLEI PLPNRPHWFL LFGATEEEIQ EICLKILQLY ARKKVDLTHL EGEVEKRKHA IEEAKAQARG LLP GG

UniProtKB: Cyclin-L2

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 45 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
40.0 mMHEPES-KOH
200.0 mMPotassium chlorideKCl
2.0 mMMagnesium chlorideMgCl2
5.0 mMbeta-mercaptoethanol
1.0 mMAMP-PNP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 36332 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: cryoSPARC (ver. 4.4.1), RELION (ver. 5.0-beta))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: AlphaFold prediction converted to cryo-EM map in Chimera X
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta) / Number images used: 783863
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 5.0-beta)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qkz:
Cryo-EM structure of CDK11B-cyclin L2-SAP30BP bound to AMP-PNP

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