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- PDB-5xon: RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS -

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Basic information

Entry
Database: PDB / ID: 5xon
TitleRNA Polymerase II elongation complex bound with Spt4/5 and TFIIS
Descriptorpart of central core
General transcription elongation factor TFIIS
Transcription elongation factor SPT4
Protein that forms a complex with Spt4p/RNA Complex
(DNA-directed RNA polymerase ...) x 2
and more 3 items
KeywordsTRANSCRIPTION/RNA / transcription / complex / TRANSCRIPTION-RNA complex
Specimen sourceKomagataella phaffii (strain gs115 / atcc 20864) / fungus / Yeast
Synthetic construct
MethodElectron microscopy (3.83 Å resolution / Particle / Single particle)
AuthorsEhara, H. / Yokoyama, T. / Shigematsu, H. / Shirouzu, M. / Sekine, S.
CitationScience, 2017, 357, 921-924

Science, 2017, 357, 921-924 StrPapers
Structure of the complete elongation complex of RNA polymerase II with basal factors.
Haruhiko Ehara / Takeshi Yokoyama / Hideki Shigematsu / Shigeyuki Yokoyama / Mikako Shirouzu / Shun-Ichi Sekine

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 29, 2017 / Release: Aug 16, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 16, 2017Structure modelrepositoryInitial release
1.1Sep 13, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: RNA polymerase II third largest subunit B44, part of central core
D: RNA polymerase II subunit B32
E: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
F: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
G: RNA polymerase II subunit
H: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
I: DNA-directed RNA polymerase subunit
J: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
K: RNA polymerase II subunit B12.5
L: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
P: RNA (30-MER)
T: DNA (48-MER)
N: DNA (48-MER)
U: General transcription elongation factor TFIIS
V: Transcription elongation factor SPT4
W: Protein that forms a complex with Spt4p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)652,13829
Polyers651,46018
Non-polymers67811
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)85560
ΔGint (kcal/M)-497
Surface area (Å2)220860

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Components

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DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI

#1: Polypeptide(L)DNA-directed RNA polymerase subunit / RNA polymerase II subunit Rpb1


Mass: 194107.422 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R4Y0, EC: 2.7.7.6
#2: Polypeptide(L)DNA-directed RNA polymerase subunit beta / RNA polymerase II subunit Rpb2


Mass: 139746.094 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4QZQ7, EC: 2.7.7.6
#9: Polypeptide(L)DNA-directed RNA polymerase subunit / RNA polymerase II subunit Rpb9


Mass: 13612.320 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4QY79

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RNA polymerase II ... , 4 types, 4 molecules CDGK

#3: Polypeptide(L)RNA polymerase II third largest subunit B44, part of central core / RNA polymerase II subunit Rpb3


Mass: 34216.293 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R7L2
#4: Polypeptide(L)RNA polymerase II subunit B32 / RNA polymerase II subunit Rpb4


Mass: 20622.980 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R2U9
#7: Polypeptide(L)RNA polymerase II subunit / RNA polymerase II subunit Rpb7


Mass: 18802.625 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R9A1
#11: Polypeptide(L)RNA polymerase II subunit B12.5 / RNA polymerase II subunit Rpb11


Mass: 13832.896 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R3Z5

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RNA polymerase subunit ... , 4 types, 4 molecules EFHJ

#5: Polypeptide(L)RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb5


Mass: 24962.680 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R3P8
#6: Polypeptide(L)RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb6


Mass: 17803.588 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R1V1
#8: Polypeptide(L)RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb8


Mass: 16249.220 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R273
#10: Polypeptide(L)RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb10


Mass: 8554.064 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R009

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Polypeptide(L) , 4 types, 4 molecules LUVW

#12: Polypeptide(L)RNA polymerase subunit, found in RNA polymerase complexes I, II, and III / RNA polymerase II subunit Rpb12


Mass: 7862.048 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4QWA8
#16: Polypeptide(L)General transcription elongation factor TFIIS


Mass: 21694.734 Da / Num. of mol.: 1 / Fragment: UNP residues 99-285
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R2R6
#17: Polypeptide(L)Transcription elongation factor SPT4


Mass: 12039.614 Da / Num. of mol.: 1 / Fragment: UNP residues 8-114
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R0E6
#18: Polypeptide(L)Protein that forms a complex with Spt4p / Spt5


Mass: 68283.984 Da / Num. of mol.: 1 / Fragment: UNP residues 206-815
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864)
References: UniProt: C4R370

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RNA chain , 1 types, 1 molecules P

#13: RNA chainRNA (30-MER)


Mass: 9492.561 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

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DNA chain , 2 types, 2 molecules TN

#14: DNA chainDNA (48-MER)


Mass: 14659.406 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#15: DNA chainDNA (48-MER)


Mass: 14917.541 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

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Non-polymers , 2 types, 11 molecules

#19: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Formula: Zn
#20: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg

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Details

Sequence detailsFOR ENTITY 9 AND 12, THE SEQUENCE REFERENCE IN UNIPROT (C4QY79 AND C4QWA8) CONTAIN ERRORS. AND AUTHOR CONFIRMED THE SEQUENCES IN THIS ENTRY ARE CORRECT.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1RNA polymerase II elongation complex bound with Spt4/5 and TFIISCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 180MULTIPLE SOURCES
2RNA polymerase IICOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 121NATURAL
3Spt4/5 and TFIISCOMPLEX16, 17, 181RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
214922Komagataella pastoris
314922Komagataella pastoris
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3607

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1GautomatchPARTICLE SELECTION1
2SerialEMIMAGE ACQUISITION1
4GctfCTF CORRECTION1
7ChimeraMODEL FITTING1
8CootMODEL FITTING1
10RELIONINITIAL EULER ASSIGNMENT1
11RELIONFINAL EULER ASSIGNMENT1
12RELIONCLASSIFICATION1
13RELION2.0.2RECONSTRUCTION1
20PhenixMODEL REFINEMENT1
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 682749 / Symmetry type: POINT
Atomic model buildingDetails: Model fitting was done with Chimera and Coot. Well-ordered regions were also refined with phenix.real_space_refine.

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