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- PDB-7emf: Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation -

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Basic information

Entry
Database: PDB / ID: 7emf
TitleHuman Mediator (deletion of MED1-IDR) in a Tail-extended conformation
Components
  • (Isoform 2 of Mediator of RNA polymerase II transcription subunit ...) x 2
  • (Mediator of RNA polymerase II transcription subunit ...) x 24
  • Unknown Chain (poly A)
KeywordsTRANSCRIPTION / Mediator complex
Function / homology
Function and homology information


positive regulation of mediator complex assembly / positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development ...positive regulation of mediator complex assembly / positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / positive regulation of chromatin binding / nuclear vitamin D receptor binding / limb development / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase binding / termination of RNA polymerase II transcription / cortical actin cytoskeleton / RSV-host interactions / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / fat cell differentiation / skeletal muscle cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / somatic stem cell population maintenance / blastocyst development / general transcription initiation factor binding / negative regulation of keratinocyte proliferation / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / negative regulation of fibroblast proliferation / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / cellular response to epidermal growth factor stimulus / lactation / Regulation of lipid metabolism by PPARalpha / positive regulation of erythrocyte differentiation / liver development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / nuclear receptor binding / nuclear estrogen receptor binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Heme signaling / brain development / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / DNA-directed 5'-3' RNA polymerase activity / protein import into nucleus / transcription corepressor activity / ubiquitin protein ligase activity / Circadian Clock / actin binding / angiogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity
Similarity search - Function
: / Mediator complex subunit 26, C-terminal domain / Mediator complex subunit 26, middle domain / Mediator of RNA polymerase II transcription subunit 26 / Mediator complex subunit 26 C-terminal / Mediator complex subunit 26 middle domain / Mediator complex, subunit Med25, PTOV domain / Mediator complex, subunit Med25, synapsin 1 / Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain / Mediator complex subunit 25, PTOV domain superfamily ...: / Mediator complex subunit 26, C-terminal domain / Mediator complex subunit 26, middle domain / Mediator of RNA polymerase II transcription subunit 26 / Mediator complex subunit 26 C-terminal / Mediator complex subunit 26 middle domain / Mediator complex, subunit Med25, PTOV domain / Mediator complex, subunit Med25, synapsin 1 / Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain / Mediator complex subunit 25, PTOV domain superfamily / Mediator complex subunit 25 PTOV activation and synapsin 2 / Mediator complex subunit 25 synapsin 1 / Mediator complex subunit 25 von Willebrand factor type A / Mediator complex, subunit Med19, metazoa / Mediator of RNA pol II transcription subunit 19 / Mediator complex, subunit Med29, metazoa / Mediator complex, subunit Med24, / : / Mediator complex subunit 24 N-terminal / Mediator complex subunit 29 / Mediator complex subunit 16, central helical bridge / Mediator complex, subunit Med23 / Mediator complex subunit 23 / Mediator of RNA polymerase II transcription subunit 15 / : / : / ARC105/Med15 mediator subunit N-terminal KIX domain / ARC105/Med15 mediator subunit central domain / ARC105/Med15 mediator subunit C-terminal domain / Mediator complex, subunit Med6, metazoa/plant / Mediator complex, subunit Med30, metazoa / Mediator complex, subunit Med28 / Mediator of RNA polymerase II transcription subunit 9, metazoan / Mediator complex subunit 30 / Mediator complex subunit 28 / Mediator of RNA polymerase II transcription subunit 14, RM2 / Mediator of RNA polymerase II transcription subunit 14, RM8 / Mediator of RNA polymerase II transcription subunit 14, RM6 / Mediator complex, subunit Med27 / Mediator complex subunit 27 / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal / : / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / Mediator complex, subunit Med7 superfmaily / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Soluble quinoprotein glucose/sorbosone dehydrogenase / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / : / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / TFIIS/LEDGF domain superfamily / Coactivator CBP, KIX domain superfamily / von Willebrand factor A-like domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 19 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 26 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 27 ...Mediator of RNA polymerase II transcription subunit 19 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 26 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 25 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 30 / Mediator of RNA polymerase II transcription subunit 15 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 28 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 9 / Mediator of RNA polymerase II transcription subunit 29 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 23 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYin, X. / Li, J. / Wu, Z. / Liu, W. / Xu, Y.
CitationJournal: Science / Year: 2021
Title: Structures of the human Mediator and Mediator-bound preinitiation complex.
Authors: Xizi Chen / Xiaotong Yin / Jiabei Li / Zihan Wu / Yilun Qi / Xinxin Wang / Weida Liu / Yanhui Xu /
Abstract: The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26- ...The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly.
History
DepositionApr 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 1
B: Unknown Chain (poly A)
D: Mediator of RNA polymerase II transcription subunit 4
F: Mediator of RNA polymerase II transcription subunit 6
G: Mediator of RNA polymerase II transcription subunit 7
H: Isoform 2 of Mediator of RNA polymerase II transcription subunit 8
I: Mediator of RNA polymerase II transcription subunit 9
J: Mediator of RNA polymerase II transcription subunit 10
K: Mediator of RNA polymerase II transcription subunit 11
N: Mediator of RNA polymerase II transcription subunit 14
O: Mediator of RNA polymerase II transcription subunit 15
P: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
Q: Mediator of RNA polymerase II transcription subunit 17
R: Mediator of RNA polymerase II transcription subunit 18
S: Mediator of RNA polymerase II transcription subunit 19
T: Mediator of RNA polymerase II transcription subunit 20
U: Mediator of RNA polymerase II transcription subunit 21
V: Mediator of RNA polymerase II transcription subunit 22
W: Mediator of RNA polymerase II transcription subunit 23
X: Mediator of RNA polymerase II transcription subunit 24
Y: Mediator of RNA polymerase II transcription subunit 25
Z: Mediator of RNA polymerase II transcription subunit 26
0: Mediator of RNA polymerase II transcription subunit 27
1: Mediator of RNA polymerase II transcription subunit 28
2: Mediator of RNA polymerase II transcription subunit 29
3: Mediator of RNA polymerase II transcription subunit 30
4: Mediator of RNA polymerase II transcription subunit 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,378,10029
Polymers1,377,96927
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area144720 Å2
ΔGint-1011 kcal/mol
Surface area328260 Å2

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Components

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Mediator of RNA polymerase II transcription subunit ... , 24 types, 24 molecules ADFGIJKNOQRSTUVWXYZ01234

#1: Protein Mediator of RNA polymerase II transcription subunit 1


Mass: 168697.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q15648
#3: Protein Mediator of RNA polymerase II transcription subunit 4


Mass: 29781.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED4 / Production host: Homo sapiens (human) / References: UniProt: Q9NPJ6
#4: Protein Mediator of RNA polymerase II transcription subunit 6


Mass: 28464.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED6 / Production host: Homo sapiens (human) / References: UniProt: O75586
#5: Protein Mediator of RNA polymerase II transcription subunit 7


Mass: 27285.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED7 / Production host: Homo sapiens (human) / References: UniProt: O43513
#7: Protein Mediator of RNA polymerase II transcription subunit 9


Mass: 16422.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED9 / Production host: Homo sapiens (human) / References: UniProt: Q9NWA0
#8: Protein Mediator of RNA polymerase II transcription subunit 10


Mass: 15710.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED10 / Production host: Homo sapiens (human) / References: UniProt: Q9BTT4
#9: Protein Mediator of RNA polymerase II transcription subunit 11


Mass: 13145.829 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED11 / Production host: Homo sapiens (human) / References: UniProt: Q9P086
#10: Protein Mediator of RNA polymerase II transcription subunit 14


Mass: 160787.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED14 / Production host: Homo sapiens (human) / References: UniProt: O60244
#11: Protein Mediator of RNA polymerase II transcription subunit 15


Mass: 86830.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED15 / Production host: Homo sapiens (human) / References: UniProt: Q96RN5
#13: Protein Mediator of RNA polymerase II transcription subunit 17


Mass: 72984.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED17 / Production host: Homo sapiens (human) / References: UniProt: Q9NVC6
#14: Protein Mediator of RNA polymerase II transcription subunit 18


Mass: 23693.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED18 / Production host: Homo sapiens (human) / References: UniProt: Q9BUE0
#15: Protein Mediator of RNA polymerase II transcription subunit 19


Mass: 26321.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED19 / Production host: Homo sapiens (human) / References: UniProt: A0JLT2
#16: Protein Mediator of RNA polymerase II transcription subunit 20


Mass: 23243.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED20 / Production host: Homo sapiens (human) / References: UniProt: Q9H944
#17: Protein Mediator of RNA polymerase II transcription subunit 21


Mass: 15575.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED21 / Production host: Homo sapiens (human) / References: UniProt: Q13503
#18: Protein Mediator of RNA polymerase II transcription subunit 22


Mass: 22243.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED22 / Production host: Homo sapiens (human) / References: UniProt: Q15528
#19: Protein Mediator of RNA polymerase II transcription subunit 23


Mass: 156652.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED23 / Production host: Homo sapiens (human) / References: UniProt: Q9ULK4
#20: Protein Mediator of RNA polymerase II transcription subunit 24


Mass: 110430.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED24 / Production host: Homo sapiens (human) / References: UniProt: O75448
#21: Protein Mediator of RNA polymerase II transcription subunit 25


Mass: 78230.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED25 / Production host: Homo sapiens (human) / References: UniProt: Q71SY5
#22: Protein Mediator of RNA polymerase II transcription subunit 26


Mass: 65544.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED26 / Production host: Homo sapiens (human) / References: UniProt: O95402
#23: Protein Mediator of RNA polymerase II transcription subunit 27


Mass: 35478.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED27 / Production host: Homo sapiens (human) / References: UniProt: Q6P2C8
#24: Protein Mediator of RNA polymerase II transcription subunit 28


Mass: 19540.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED28 / Production host: Homo sapiens (human) / References: UniProt: Q9H204
#25: Protein Mediator of RNA polymerase II transcription subunit 29


Mass: 21089.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED29 / Production host: Homo sapiens (human) / References: UniProt: Q9NX70
#26: Protein Mediator of RNA polymerase II transcription subunit 30


Mass: 20301.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED30 / Production host: Homo sapiens (human) / References: UniProt: Q96HR3
#27: Protein Mediator of RNA polymerase II transcription subunit 31


Mass: 15826.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED31 / Production host: Homo sapiens (human) / References: UniProt: Q9Y3C7

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Isoform 2 of Mediator of RNA polymerase II transcription subunit ... , 2 types, 2 molecules HP

#6: Protein Isoform 2 of Mediator of RNA polymerase II transcription subunit 8


Mass: 29112.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED8 / Production host: Homo sapiens (human) / References: UniProt: Q96G25
#12: Protein Isoform 2 of Mediator of RNA polymerase II transcription subunit 16


Mass: 93136.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED16 / Production host: Homo sapiens (human) / References: UniProt: Q9Y2X0

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Protein/peptide / Non-polymers , 2 types, 3 molecules B

#28: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#2: Protein/peptide Unknown Chain (poly A)


Mass: 1439.571 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Structure of the human Mediator complex / Type: COMPLEX / Entity ID: #1-#27 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 32

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95433 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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