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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RTF1 PLUS3 DOMAIN IN COMPLEX WITH SPT5 CTR PHOSPHOPEPTIDE
 
Authors :  A. D. Wier, A. Heroux, A. P. Vandemark
Date :  03 Jun 13  (Deposition) - 02 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  B,G  (1x)
Biol. Unit 2:  C,H  (1x)
Biol. Unit 3:  E,I  (1x)
Biol. Unit 4:  F,J  (1x)
Biol. Unit 5:  A  (1x)
Biol. Unit 6:  D  (1x)
Keywords :  Tutor, Plus3, Peptide Binding Protein, Spt5 Ctr Binding, Transcription, Paf1 Complex, Rtf1, Orf Association Region, Chromatin, Transcription-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Wier, M. K. Mayekar, A. Heroux, K. M. Arndt, A. P. Vandemark
Structural Basis For Spt5-Mediated Recruitment Of The Paf1 Complex To Chromatin.
Proc. Natl. Acad. Sci. Usa V. 110 17290 2013
PubMed-ID: 24101474  |  Reference-DOI: 10.1073/PNAS.1314754110

(-) Compounds

Molecule 1 - RNA POLYMERASE-ASSOCIATED PROTEIN RTF1 HOMOLOG
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLC3
    Expression System Strain: BL21(DE3) CODON+RILP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PLUS3, UNP RESIDUES 353-484
    Gene: KIAA0252, RTF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - TRANSCRIPTION ELONGATION FACTOR SPT5
    Chains: G, H, I, J
    Engineered: YES
    Fragment: CTR, UNP RESIDUES 778-790
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMAN SPT5
    Synonym: HSPT5, DRB SENSITIVITY-INDUCING FACTOR 160 KDA SUBUNIT, DSIF P160, DRB SENSITIVITY-INDUCING FACTOR LARGE SUBUNIT, DSIF LARGE SUBUNIT, TAT-COTRANSACTIVATOR 1 PROTEIN, TAT-CT1 PROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x):  B    G   
Biological Unit 2 (1x):   C    H  
Biological Unit 3 (1x):     E   I 
Biological Unit 4 (1x):      F   J
Biological Unit 5 (1x): A         
Biological Unit 6 (1x):    D      

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 37)

Asymmetric Unit (3, 37)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO429Ligand/IonSULFATE ION
3TPO4Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 4 (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 5 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
3TPO-1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 6 (2, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
3TPO-1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:401 , ASP A:433 , ARG A:435 , PHE A:437BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREARG A:366 , SER A:443 , ASN A:444 , GLN A:445 , ARG H:783BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREVAL A:414 , TYR A:415 , GLN A:416BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREARG A:363 , SER A:365 , HIS A:367 , LYS A:368 , GLN C:416BINDING SITE FOR RESIDUE GOL A 504
05AC5SOFTWAREARG B:366 , GLU B:370 , GLY B:418 , HOH B:602 , ARG D:366 , GLU D:370 , GLY D:418 , HOH D:603BINDING SITE FOR RESIDUE SO4 B 501
06AC6SOFTWARETHR B:411 , ALA B:412 , ARG B:438BINDING SITE FOR RESIDUE SO4 B 502
07AC7SOFTWAREHIS B:374 , THR B:422 , ASN B:423 , LYS B:424BINDING SITE FOR RESIDUE SO4 B 503
08AC8SOFTWAREHIS B:394 , ASN B:395BINDING SITE FOR RESIDUE SO4 B 504
09AC9SOFTWAREARG B:401 , LEU B:428 , ARG B:429 , HIS B:430 , ASP B:433 , ARG B:435 , PHE B:437BINDING SITE FOR RESIDUE SO4 B 505
10BC1SOFTWARETHR B:448 , GLU B:449 , HOH B:608BINDING SITE FOR RESIDUE SO4 B 506
11BC2SOFTWAREGLN B:416BINDING SITE FOR RESIDUE SO4 B 507
12BC3SOFTWAREARG C:363 , SER C:365 , LYS C:368BINDING SITE FOR RESIDUE SO4 C 501
13BC4SOFTWAREHIS C:374 , THR C:422 , ASN C:423 , LYS C:424BINDING SITE FOR RESIDUE SO4 C 502
14BC5SOFTWARETHR C:448 , GLU C:449BINDING SITE FOR RESIDUE SO4 C 503
15BC6SOFTWAREARG A:366 , GLU A:370 , ARG C:366 , GLU C:370 , GLY C:418 , HOH C:612BINDING SITE FOR RESIDUE SO4 C 504
16BC7SOFTWAREPHE C:377 , PHE C:378 , ALA C:379 , LYS C:380 , HIS F:394BINDING SITE FOR RESIDUE GOL C 505
17BC8SOFTWAREGLN B:416 , ARG D:363 , SER D:365BINDING SITE FOR RESIDUE SO4 D 501
18BC9SOFTWAREARG D:366 , TYR D:400 , SER D:443 , ASN D:444 , GLN D:445 , ARG G:783BINDING SITE FOR RESIDUE SO4 D 502
19CC1SOFTWAREARG D:401 , LYS D:454 , HOH D:618BINDING SITE FOR RESIDUE SO4 D 503
20CC2SOFTWAREARG D:361 , ASN D:473 , ASN F:432BINDING SITE FOR RESIDUE SO4 D 504
21CC3SOFTWAREARG D:401 , HIS D:430 , ASP D:433 , ARG D:435 , PHE D:437BINDING SITE FOR RESIDUE SO4 D 505
22CC4SOFTWARETHR D:448 , GLU D:449BINDING SITE FOR RESIDUE SO4 D 506
23CC5SOFTWARETYR D:415 , GLN D:416 , ARG D:421BINDING SITE FOR RESIDUE SO4 D 507
24CC6SOFTWAREARG B:363 , SER B:365 , LYS B:368 , ARG B:371 , HOH B:615 , GLN D:416BINDING SITE FOR RESIDUE GOL D 508
25CC7SOFTWAREARG E:401 , LYS E:454BINDING SITE FOR RESIDUE SO4 E 501
26CC8SOFTWAREARG E:366 , GLU E:370 , GLY E:418 , HOH E:611 , ARG I:783BINDING SITE FOR RESIDUE SO4 E 502
27CC9SOFTWAREASN B:393 , HIS E:394 , ASN E:395BINDING SITE FOR RESIDUE SO4 E 503
28DC1SOFTWAREARG E:401 , ARG E:429 , HIS E:430 , ASP E:433 , ARG E:435 , PHE E:437BINDING SITE FOR RESIDUE SO4 E 504
29DC2SOFTWARETHR E:448 , GLU E:449 , HOH E:609BINDING SITE FOR RESIDUE SO4 E 505
30DC3SOFTWAREARG F:366 , GLU F:370 , GLY F:418 , SER J:782BINDING SITE FOR RESIDUE SO4 F 501
31DC4SOFTWARETHR F:448 , GLU F:449BINDING SITE FOR RESIDUE SO4 F 502
32DC5SOFTWARETHR F:411 , ALA F:412 , LYS F:413 , ARG F:438BINDING SITE FOR RESIDUE SO4 F 503
33DC6SOFTWARESER F:365 , LYS F:368 , ARG F:371BINDING SITE FOR RESIDUE GOL F 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L1U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4L1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L1U)

(-) Exons   (0, 0)

(no "Exon" information available for 4L1U)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh.hhhhhhhhh...hhhhhhh..eeeee....eeeeeeeeeeeeeeeeee..eeeeeeeeeee..eeeeee.hhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1u A 349 ITHMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEAL 483
                                   358       368       378       388    || 403       413       423       433       443       453       463       473       483
                                                                      393|                                                                                    
                                                                       399                                                                                    


Chain B from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh...hhhhhhhhh...hhhhhhh..eeeeeeeee..eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee..eeeeee.hhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1u B 350 THMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEAL 483
                                   359       369       379       389       399       409       419       429       439       449       459       469       479    


Chain C from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh...hhhhhhhhh...hhhhhhh..eeeee.....eeeeeeeeeeeeeeeeee..eeeeeeeeeee..eeeeee.hhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1u C 350 THMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEAL 483
                                   359       369       379       389  ||   403       413       423       433       443       453       463       473       483
                                                                    392|                                                                                      
                                                                     397                                                                                      


Chain D from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh.hhhhhhhhh...hhhhhhh..eeeeeeeee..eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee..eeeeee.hhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1u D 349 ITHMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEALN 484
                                   358       368       378       388       398       408       418       428       438       448       458       468       478      


Chain E from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh.hhhhhhhhh...hhhhhhh..eeeeeeeee..eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee..eeeeee.hhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1u E 349 ITHMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEA 482
                                   358       368       378       388       398       408       418       428       438       448       458       468       478    


Chain F from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh.hhhhhhhhh...hhhhhhh..eeeeeeeee..eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee..eeeeehhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1u F 349 ITHMVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEA 482
                                   358       368       378       388       398       408       418       428       438       448       458       468       478    


Chain G from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4l1u G 781 GSRtPMYG 788
                               |    
                             784-TPO


Chain H from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ......hhhhh Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4l1u H 780 SGSRtPMYGSQ 790
                                |  789 
                              784-TPO  


Chain I from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4l1u I 783 RtPMY 787
                             |   
                           784-TPO


Chain J from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4l1u J 782 SRtPM 786
                              |  
                              |  
                            784-TPO
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

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(no "SCOP Domain" information available for 4L1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L1U)

(-) Gene Ontology  (37, 45)

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  4l1u
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  SPT5H_HUMAN | O00267
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Access by UniProt ID/Accession number
  RTF1_HUMAN | Q92541
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SPT5H_HUMAN | O00267
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RTF1_HUMAN | Q92541: 2bze 2db9 3u1u 4l1p
        SPT5H_HUMAN | O00267: 2do3 2e6z 2e70 3h7h

(-) Related Entries Specified in the PDB File

4l1p THE APO FORM OF THE PLUS3 DOMAIN.