6GML Transcription date May 27, 2018
title Structure Of Paused Transcription Complex Pol II-Dsif-Nelf
authors S.M.Vos, L.Farnung, H.Urlaub, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase Subunit
Chain: A
Ec: 2.7.7.6
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: B
Ec: 2.7.7.6

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit C
Chain: C

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit E
Chain: E

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit F
Chain: F

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9,Dna-Directed Rna Poly Subunit I,Rna Polymerase II 14.5 Kda Subunit,Rpb14.5;

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Uncharacterized Protein
Chain: J

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Uncharacterized Protein
Chain: K

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Uncharacterized Protein
Chain: L

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Non-Template Dna
Chain: N
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Other_details: Mutated From Original Sequence For Structura

Molecule: Tar Rna
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676

Molecule: Template Dna
Chain: T
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676

Molecule: Negative Elongation Factor A
Chain: U
Synonym: Nelf-A,Wolf-Hirschhorn Syndrome Candidate 2 Protei
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nelfa, Whsc2, Pokcl.15
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: 438a

Molecule: Negative Elongation Factor B,Negative Elongation
Chain: V
Synonym: Nelf-B,Cofactor Of Brca1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nelfb, Cobra1, Kiaa1182
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: 438a

Molecule: Negative Elongation Factor Cd
Chain: W
Synonym: Nelf-Cd,Th1-Like Protein
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nelfcd, Nelfd, Th1, Th1l, Hspc130
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: 438b

Molecule: Negative Elongation Factor E,Negative Elongation
Chain: X
Synonym: Nelf-E,Rna-Binding Protein Rd
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nelfe, Rd, Rdbp
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: 438a

Molecule: Transcription Elongation Factor Spt4
Chain: Y
Synonym: Hspt4,Drb Sensitivity-Inducing Factor 14 Kda Subun P14,Drb Sensitivity-Inducing Factor Small Subunit,Dsif Smal
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Supt4h1, Spt4h, Supt4h
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Ril

Molecule: Transcription Elongation Factor Spt5
Chain: Z
Synonym: Hspt5,Drb Sensitivity-Inducing Factor 160 Kda Subu P160,Drb Sensitivity-Inducing Factor Large Subunit,Dsif Lar Subunit,Tat-Cotransactivator 1 Protein,Tat-Ct1 Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Supt5h, Spt5, Spt5h
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Ril

Molecule: Rna Polymerase II Subunit D
Chain: D

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus

Molecule: Rna Polymerase II Subunit G
Chain: G

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Thymus
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.20 Å
ligand
enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K


L


U


V


W


X


Y


Z


Primary referenceStructure of paused transcription complex Pol II-DSIF-NELF., Vos SM, Farnung L, Urlaub H, Cramer P, Nature. 2018 Aug;560(7720):601-606. doi: 10.1038/s41586-018-0442-2. Epub 2018 Aug, 22. PMID:30135580
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (838 Kb) [Save to disk]
  • Biological Unit Coordinates (6gml.pdb1.gz) 815 Kb
  • CSU: Contacts of Structural Units for 6GML
  • Retrieve 6GML in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6GML from S2C, [Save to disk]
  • View 6GML in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6GML
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6gml from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6gml_I] [6gml_E] [6gml_X] [6gml_N] [6gml_D] [6gml_P] [6gml_K] [6gml_G] [6gml_U] [6gml_J] [6gml_W] [6gml_V] [6gml_A] [6gml_Z] [6gml_B] [6gml_Y] [6gml_F] [6gml_L] [6gml_C] [6gml_H] [6gml_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6GML
  • Community annotation for 6GML at PDBWiki (http://pdbwiki.org)

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