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- EMDB-53027: Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP -

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Basic information

Entry
Database: EMDB / ID: EMD-53027
TitleCryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP
Map dataPost-processed, sharpened cryo-EM map.
Sample
  • Complex: CAK-CDK2-cyclin A2 complex
    • Complex: CDK-activating kinase (CAK)
      • Protein or peptide: CDK-activating kinase assembly factor MAT1
      • Protein or peptide: Cyclin-H
      • Protein or peptide: Cyclin-dependent kinase 7
    • Complex: CDK2-cyclin A2
      • Protein or peptide: Cyclin-dependent kinase 2
      • Protein or peptide: Cyclin-A2
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsComplex / cell cycle / kinase / TRANSFERASE
Function / homology
Function and homology information


: / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / cyclin A2-CDK1 complex / ventricular system development / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 ...: / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / cyclin A2-CDK1 complex / ventricular system development / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / male pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / female pronucleus / cellular response to cocaine / [RNA-polymerase]-subunit kinase / response to glucagon / RNA Polymerase I Transcription Termination / positive regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / RNA Pol II CTD phosphorylation and interaction with CE / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / 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 / X chromosome / mRNA Capping / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / microtubule organizing center / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / regulation of DNA replication / telomere maintenance in response to DNA damage / centrosome duplication / RNA Polymerase I Transcription Initiation / regulation of G1/S transition of mitotic cell cycle / G0 and Early G1 / cochlea development / RNA polymerase II transcribes snRNA genes / Telomere Extension By Telomerase / animal organ regeneration / Activation of the pre-replicative complex / ATP-dependent activity, acting on DNA / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Tat-mediated elongation of the HIV-1 transcript / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Formation of HIV-1 elongation complex containing HIV-1 Tat / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Activation of ATR in response to replication stress / 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 / condensed chromosome / cellular response to platelet-derived growth factor stimulus / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / RNA Polymerase II Pre-transcription Events / positive regulation of smooth muscle cell proliferation / RNA polymerase II CTD heptapeptide repeat kinase activity / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RNA Polymerase I Promoter Escape
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-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain ...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-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / 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-A2 / Cyclin-dependent kinase 2 / Cyclin-dependent kinase 7 / Cyclin-H / CDK-activating kinase assembly factor MAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsCushing VI / Greber BJ / McGeoch AJS / Feng J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
The Institute of Cancer Research (ICR) United Kingdom
CitationJournal: To Be Published
Title: Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase
Authors: Cushing VI / Greber BJ / McGeoch AJS / Feng J
History
DepositionMar 5, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53027.png

Downloads & links

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Map

FileDownload / File: emd_53027.map.gz / Format: CCP4 / Size: 48.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed, sharpened cryo-EM map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 234 pix.
= 255.42 Å		1.09 Å/pix.
x 234 pix.
= 255.42 Å		1.09 Å/pix.
x 234 pix.
= 255.42 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09154 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.088064834 - 0.1606322
Average (Standard dev.)0.000023019655 (±0.0047325743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions234234234
Spacing234234234
CellA=B=C: 255.42035 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53027_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map.

Fileemd_53027_half_map_1.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map.

Fileemd_53027_half_map_2.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CAK-CDK2-cyclin A2 complex

EntireName: CAK-CDK2-cyclin A2 complex
Components
  • Complex: CAK-CDK2-cyclin A2 complex
    • Complex: CDK-activating kinase (CAK)
      • Protein or peptide: CDK-activating kinase assembly factor MAT1
      • Protein or peptide: Cyclin-H
      • Protein or peptide: Cyclin-dependent kinase 7
    • Complex: CDK2-cyclin A2
      • Protein or peptide: Cyclin-dependent kinase 2
      • Protein or peptide: Cyclin-A2
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: CAK-CDK2-cyclin A2 complex

SupramoleculeName: CAK-CDK2-cyclin A2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: CDK-activating kinase (CAK) in complex with CDK2-cyclin A2 in the presence of nucleotide analogue AMP-PNP
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83 KDa

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Supramolecule #2: CDK-activating kinase (CAK)

SupramoleculeName: CDK-activating kinase (CAK) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#5 / Details: CAK complex bound to nucleotide analogue AMP-PNP
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: CDK2-cyclin A2

SupramoleculeName: CDK2-cyclin A2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Details: CDK2-cyclin A2 complex bound to nucleotide analogue AMP-PNP
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cyclin-dependent kinase 2

MacromoleculeName: Cyclin-dependent kinase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.24875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMENFQKV EKIGEGTYGV VYKARNKLTG EVVALKKIRL DTETEGVPST AIREISLLKE LNHPNIVKLL DVIHTENKLY LVFEFLHQD LKKFMDASAL TGIPLPLIKS YLFQLLQGLA FCHSHRVLHR DLKPQNLLIN TEGAIKLADF GLARAFGVPV R TYTHEVVT ...String:
SNAMENFQKV EKIGEGTYGV VYKARNKLTG EVVALKKIRL DTETEGVPST AIREISLLKE LNHPNIVKLL DVIHTENKLY LVFEFLHQD LKKFMDASAL TGIPLPLIKS YLFQLLQGLA FCHSHRVLHR DLKPQNLLIN TEGAIKLADF GLARAFGVPV R TYTHEVVT LWYRAPEILL GCKYYSTAVD IWSLGCIFAE MVTRRALFPG DSEIDQLFRI FRTLGTPDEV VWPGVTSMPD YK PSFPKWA RQDFSKVVPP LDEDGRSLLS QMLHYDPNKR ISAKAALAHP FFQDVTKPVP HLRL

UniProtKB: Cyclin-dependent kinase 2

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Macromolecule #2: Cyclin-A2

MacromoleculeName: Cyclin-A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.867805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMLGNSAP GPATREAGSA LLALQQTALQ EDQENINPEK AAPVQQPRTR AALAVLKSGN PRGLAQQQRP KTRRVAPLKD LPVNDEHVT VPPWKANSKQ PAFTIHVDEA EKEAQKKPAE SQKIEREDAL AFNSAISLPG PRKPLVPLDY PMDGSFESPH T MDMSIVLE ...String:
SNAMLGNSAP GPATREAGSA LLALQQTALQ EDQENINPEK AAPVQQPRTR AALAVLKSGN PRGLAQQQRP KTRRVAPLKD LPVNDEHVT VPPWKANSKQ PAFTIHVDEA EKEAQKKPAE SQKIEREDAL AFNSAISLPG PRKPLVPLDY PMDGSFESPH T MDMSIVLE DEKPVSVNEV PDYHEDIHTY LREMEVKCKP KVGYMKKQPD ITNSMRAILV DWLVEVGEEY KLQNETLHLA VN YIDRFLS SMSVLRGKLQ LVGTAAMLLA SKFEEIYPPE VAEFVYITDD TYTKKQVLRM EHLVLKVLTF DLAAPTVNQF LTQ YFLHQQ PANCKVESLA MFLGELSLID ADPYLKYLPS VIAGAAFHLA LYTVTGQSWP ESLIRKTGYT LESLKPCLMD LHQT YLKAP QHAQQSIREK YKNSKYHGVS LLNPPETLNL

UniProtKB: Cyclin-A2

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Macromolecule #3: CDK-activating kinase assembly factor MAT1

MacromoleculeName: CDK-activating kinase assembly factor MAT1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.13234 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDK EVEIRKKVLK IYNKREEDFP SLREYNDFLE EVEEIVFNLT NNVDLDNTKK KMEIYQKENK DVIQKNKLKL T REQEELEE ...String:
MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDK EVEIRKKVLK IYNKREEDFP SLREYNDFLE EVEEIVFNLT NNVDLDNTKK KMEIYQKENK DVIQKNKLKL T REQEELEE ALEVERQENE QRRLFIQKEE QLQQILKRKN KQAFLDELES SDLPVALLLA QHKDRSTQLE MQLEKPKPVK PV TFSTGIK MGQHISLAPI HKLEEALYEY QPLQIETYGP HVPELEMLGR LGYLNHVRAA SPQDLAGGYT SSLACHRALQ DAF SGLFWQ PS

UniProtKB: CDK-activating kinase assembly factor MAT1

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Macromolecule #4: Cyclin-H

MacromoleculeName: Cyclin-H / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.721508 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: (ACE)MYHNSSQKR HWTFSSEEQL ARLRADANRK FRCKAVANGK VLPNDPVFLE PHEEMTLCKY YEKRLLEFCS VFKPAM PRS VVGTACMYFK RFYLNNSVME YHPRIIMLTC AFLACKVDEF NVSSPQFVGN LRESPLGQEK ALEQILEYEL LLIQQLN FH LIVHNPYRPF ...String:
(ACE)MYHNSSQKR HWTFSSEEQL ARLRADANRK FRCKAVANGK VLPNDPVFLE PHEEMTLCKY YEKRLLEFCS VFKPAM PRS VVGTACMYFK RFYLNNSVME YHPRIIMLTC AFLACKVDEF NVSSPQFVGN LRESPLGQEK ALEQILEYEL LLIQQLN FH LIVHNPYRPF EGFLIDLKTR YPILENPEIL RKTADDFLNR IALTDAYLLY TPSQIALTAI LSSASRAGIT MESYLSES L MLKENRTCLS QLLDIMKSMR NLVKKYEPPR SEEVAVLKQK LERCHSAELA LNVITKKRKG YEDDDYVSKK SKHEEEEWT DDDLVESL

UniProtKB: Cyclin-H

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Macromolecule #5: Cyclin-dependent kinase 7

MacromoleculeName: Cyclin-dependent kinase 7 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.65107 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIK LGHRSEAKDG INRTALREIK LLQELSHPNI IGLLDAFGHK SNISLVFDFM ETDLEVIIKD NSLVLTPSHI K AYMLMTLQ ...String:
MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIK LGHRSEAKDG INRTALREIK LLQELSHPNI IGLLDAFGHK SNISLVFDFM ETDLEVIIKD NSLVLTPSHI K AYMLMTLQ GLEYLHQHWI LHRDLKPNNL LLDENGVLKL ADFGLAKSFG SPNRAYTHQV VTRWYRAPEL LFGARMYGVG VD MWAVGCI LAELLLRVPF LPGDSDLDQL TRIFETLGTP TEEQWPDMCS LPDYVTFKSF PGIPLHHIFS AAGDDLLDLI QGL FLFNPC ARITATQALK MKYFSNRPGP TPGCQLPRPN CPVETLKEQS NPALAIKRKR TEALEQGGLP KKLIF

UniProtKB: Cyclin-dependent kinase 7

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Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / 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 #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 49 / 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

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMSodium chlorideNaCl
10.0 mMMagnesium chlorideMgCl2
0.5 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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 33998 / Average electron dose: 50.0 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: 2.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 130000
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, RELION (ver. 4.0)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 282506
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0)

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Atomic model buiding 1

Initial model
PDB IDChain

8p6y

source_name: PDB, initial_model_type: experimental model

1okv

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qcv:
Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP

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