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- PDB-6j51: RNA polymerase II elongation complex bound with Spt4/5 and foreig... -

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Entry
Database: PDB / ID: 6j51
TitleRNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position)
Components
  • (DNA (198-MER)) x 2
  • (DNA (36-MER)) x 2
  • (DNA-directed RNA polymerase ...) x 3
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ...) x 4
  • (Transcription elongation factor ...) x 2
  • DNA-directed RNA polymerases I, II, and III subunit RPABC3
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.3
  • Histone H4
  • Protein that forms a complex with Spt4p
  • RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
KeywordsTRANSCRIPTION/RNA/DNA / nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex
Function / homology
Function and homology information


regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / RPB4-RPB7 complex / chromatin-protein adaptor activity / pericentric heterochromatin formation / inner kinetochore ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / RPB4-RPB7 complex / chromatin-protein adaptor activity / pericentric heterochromatin formation / inner kinetochore / transcription elongation factor activity / muscle cell differentiation / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / transcription elongation-coupled chromatin remodeling / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nucleus organization / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / spermatid development / transcription initiation at RNA polymerase I promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / chromosome, centromeric region / single fertilization / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / protein localization to CENP-A containing chromatin / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / Replacement of protamines by nucleosomes in the male pronucleus / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / translation initiation factor binding / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / embryo implantation / telomere organization / DNA-directed RNA polymerase activity / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / transcription elongation factor complex / regulation of DNA-templated transcription elongation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / lipopolysaccharide binding / Transcriptional regulation by small RNAs / P-body / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / ribonucleoside binding / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / : / : / :
Similarity search - Function
Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription elongation factor SPT5, KOWx domain ...Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / S1 RNA binding domain / S1 domain
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / Transcription elongation factor 1 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT4 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III ...DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / Transcription elongation factor 1 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT4 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / Transcription elongation factor SPT5 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / DNA-directed RNA polymerase subunit / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsEhara, H. / Kujirai, T. / Fujino, Y. / Shirouzu, M. / Kurumizaka, H. / Sekine, S.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25116002 Japan
Japan Society for the Promotion of ScienceJP15H04344 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101082 Japan
Japan Science and TechnologyJPMJCR16G1 Japan
CitationJournal: Science / Year: 2019
Title: Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Authors: Haruhiko Ehara / Tomoya Kujirai / Yuka Fujino / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine /
Abstract: RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional ...RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

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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: DNA-directed RNA polymerases I, II, and III subunit RPABC3
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 ABC10-alpha
P: RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
T: DNA (198-MER)
N: DNA (198-MER)
M: Transcription elongation factor 1 homolog
V: Transcription elongation factor SPT4
W: Protein that forms a complex with Spt4p
a: Histone H3.3
b: Histone H4
c: Histone H2A type 1-B/E
d: Histone H2B type 1-J
e: Histone H3.3
f: Histone H4
g: Histone H2A type 1-B/E
h: Histone H2B type 1-J
0: DNA (36-MER)
1: DNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)898,65639
Polymers897,97828
Non-polymers67811
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein DNA-directed RNA polymerase subunit


Mass: 194107.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R4Y0, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 139746.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZQ7, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit


Mass: 13612.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (fungus)
Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1
References: UniProt: F2QPE6

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

#3: Protein RNA polymerase II third largest subunit B44, part of central core


Mass: 34216.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2
#4: Protein RNA polymerase II subunit B32


Mass: 20622.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R2U9
#7: Protein RNA polymerase II subunit


Mass: 18802.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R9A1
#11: Protein RNA polymerase II subunit B12.5


Mass: 13832.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5

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

#5: Protein RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III


Mass: 24962.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8
#6: Protein RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III


Mass: 17803.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1
#10: Protein RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III


Mass: 8554.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R009
#12: Protein RNA polymerase subunit ABC10-alpha


Mass: 7862.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (fungus)
Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1
References: UniProt: F2QMI1

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Protein , 6 types, 10 molecules HWaebfcgdh

#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 16249.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R273
#18: Protein Protein that forms a complex with Spt4p / Spt5


Mass: 101459.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / Gene: PAS_chr3_1136 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R370
#19: Protein Histone H3.3


Mass: 15643.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243
#20: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#21: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#22: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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RNA chain , 1 types, 1 molecules P

#13: RNA chain RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')


Mass: 5124.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA chain , 4 types, 4 molecules TN01

#14: DNA chain DNA (198-MER)


Mass: 60869.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA (198-MER)


Mass: 61381.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: DNA chain DNA (36-MER)


Mass: 11053.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#24: DNA chain DNA (36-MER)


Mass: 11100.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Transcription elongation factor ... , 2 types, 2 molecules MV

#16: Protein Transcription elongation factor 1 homolog / Elf1


Mass: 12606.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / Gene: PAS_c121_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: C4QZ45
#17: Protein Transcription elongation factor SPT4


Mass: 12039.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-1_0350 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0E6

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Non-polymers , 2 types, 11 molecules

#25: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#26: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position)
Type: COMPLEX / Entity ID: #1-#24 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Komagataella phaffii (fungus) / Strain: strain GS115 / ATCC 20864
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: 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 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
13RELION3.0-beta23D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31784 / Symmetry type: POINT

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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

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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

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