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 Microscopy	resolution	3.20 Å
ligand	MG, ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
Gene Ontology	Chain Function Process Component A B C D E F G H I J K L U V W X Y Z
Primary reference	Structure 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 LPC: Ligand-Protein Contacts for 6GML 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

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

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)

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---