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(-) Description

Title :  STRUCTURE OF THE HUMAN SRP S DOMAIN WITH SRP72 RNA-BINDING DOMAIN
 
Authors :  M. M. M. Becker, K. Wild, I. Sinning
Date :  26 Oct 16  (Deposition) - 07 Dec 16  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Protein Targeting, Signal Recognition Particle, Protein-Rna Complex, Rna Kink-Turn, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Becker, K. Lapouge, B. Segnitz, K. Wild, I. Sinning
Structures Of Human Srp72 Complexes Provide Insights Into Srp Rna Remodeling And Ribosome Interaction.
Nucleic Acids Res. V. 45 470 2017
PubMed-ID: 27899666  |  Reference-DOI: 10.1093/NAR/GKW1124

(-) Compounds

Molecule 1 - HUMAN GENE FOR SMALL CYTOPLASMIC 7SL RNA (7L30.1)
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SRP19
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP19
 
Molecule 3 - SIGNAL RECOGNITION PARTICLE SUBUNIT SRP68
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SRP68
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP68,SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN
 
Molecule 4 - SIGNAL RECOGNITION PARTICLE SUBUNIT SRP72
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SRP72
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP72,SIGNAL RECOGNITION PARTICLE 72 KDA PROTEIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 66)

Asymmetric Unit (4, 66)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3K10Ligand/IonPOTASSIUM ION
4MG45Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3K-1Ligand/IonPOTASSIUM ION
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3K-1Ligand/IonPOTASSIUM ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (52, 52)

Asymmetric Unit (52, 52)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:194 , U A:195 , G A:204 , K A:328binding site for residue MG A 301
02AC2SOFTWAREU A:132 , G A:164binding site for residue MG A 302
03AC3SOFTWAREG A:238 , G A:239binding site for residue MG A 303
04AC4SOFTWAREU A:241binding site for residue MG A 304
05AC5SOFTWAREG A:177 , G A:178binding site for residue MG A 305
06AC6SOFTWAREC A:196 , G A:198binding site for residue MG A 309
07AC7SOFTWAREG A:198binding site for residue MG A 310
08AC8SOFTWAREG A:175binding site for residue MG A 311
09AC9SOFTWAREG A:152binding site for residue MG A 312
10AD1SOFTWAREG A:168 , SER C:157binding site for residue MG A 314
11AD2SOFTWAREG A:238binding site for residue MG A 315
12AD3SOFTWAREC A:129 , A A:130binding site for residue MG A 316
13AD4SOFTWAREG A:237 , G A:238binding site for residue MG A 317
14AD5SOFTWAREG A:209 , G A:210 , K A:332binding site for residue MG A 318
15AD6SOFTWAREC A:220binding site for residue MG A 319
16AD7SOFTWAREA A:184binding site for residue MG A 320
17AD8SOFTWAREC A:111binding site for residue MG A 321
18AD9SOFTWAREU A:132binding site for residue MG A 322
19AE1SOFTWAREGOL A:333binding site for residue MG A 324
20AE2SOFTWAREG A:210binding site for residue MG A 325
21AE3SOFTWAREG A:193 , G A:194 , U A:195 , MG A:301binding site for residue K A 328
22AE4SOFTWAREG A:109 , U A:110 , U A:241 , G A:243 , C A:244binding site for residue K A 329
23AE5SOFTWAREGOL A:335binding site for residue K A 330
24AE6SOFTWAREGOL A:336binding site for residue K A 331
25AE7SOFTWAREC A:185 , G A:210 , U A:211 , MG A:318binding site for residue K A 332
26AE8SOFTWAREC A:191 , A A:205 , G A:206 , MG A:324binding site for residue GOL A 333
27AE9SOFTWAREA A:127 , U A:128 , C A:221 , G A:222 , U A:223binding site for residue GOL A 334
28AF1SOFTWAREG A:179 , U A:181 , K A:330 , GOL A:337binding site for residue GOL A 335
29AF2SOFTWAREC A:189 , A A:205 , K A:331binding site for residue GOL A 336
30AF3SOFTWAREG A:179 , G A:180 , A A:216 , C A:217 , U A:218 , GOL A:335binding site for residue GOL A 337
31AF4SOFTWAREASN B:59 , GLN B:88binding site for residue GOL B 201
32AF5SOFTWAREGLN C:70 , ARG C:236 , GLU C:239binding site for residue MG C 302
33AF6SOFTWAREU A:167binding site for residue MG C 303
34AF7SOFTWAREU E:132 , G E:164binding site for residue MG E 301
35AF8SOFTWAREG E:235binding site for residue MG E 302
36AF9SOFTWAREU E:211binding site for residue MG E 303
37AG1SOFTWAREG E:146binding site for residue MG E 304
38AG2SOFTWAREG E:135 , G E:136binding site for residue MG E 305
39AG3SOFTWAREC E:185 , A E:208 , G E:209binding site for residue MG E 307
40AG4SOFTWAREG E:206binding site for residue MG E 308
41AG5SOFTWAREG E:238 , G E:239binding site for residue MG E 309
42AG6SOFTWAREU E:236 , G E:237binding site for residue MG E 310
43AG7SOFTWAREG E:198binding site for residue MG E 311
44AG8SOFTWAREG E:198binding site for residue MG E 312
45AG9SOFTWAREG E:194 , U E:195 , G E:204 , GOL E:321binding site for residue K E 315
46AH1SOFTWAREU E:181 , GOL E:320binding site for residue K E 316
47AH2SOFTWAREU E:223binding site for residue K E 317
48AH3SOFTWAREC E:217 , U E:218 , GOL E:322binding site for residue K E 318
49AH4SOFTWAREG E:109 , U E:110 , U E:241 , G E:243binding site for residue K E 319
50AH5SOFTWAREG E:179 , G E:180 , U E:181 , K E:316 , GOL E:322binding site for residue GOL E 320
51AH6SOFTWAREA E:192 , G E:193 , G E:203 , G E:204 , K E:315binding site for residue GOL E 321
52AH7SOFTWAREG E:178 , G E:179 , K E:318 , GOL E:320binding site for residue GOL E 322

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M73)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5M73)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M73)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M73)

(-) Exons   (0, 0)

(no "Exon" information available for 5M73)

(-) 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:RNA  Length:145
                                                                                                                                                                                 
                 5m73 A 105 gGGUGUCCGCACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGGGAUCGCGCCUA 249
                            |      114       124       134       144       154       164       174       184       194       204       214       224       234       244     
                            |                                                                                                                                                
                          105-GTP                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhheeehhhhhh...hhhhh............hhhhhhhhhhhh...eeee.................eeee...............hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5m73 B  11 DQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTR 118
                                    20        30        40        50        60        70        80        90       100       110        


Chain C from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh................hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m73 C  58 HHLEILQIIKESQQQHGLRHGDFQRYRGYCSRRQRRLRKTLNFKMGNRHKFTGKKVTEDLLTDNRYLLLVLMDAERAWSYAMQLKQEANTEPRKRFHLLSRLRKAVKHAEELERLCESNRVDAKTKLEAQAYTAYLSGMLRFEHQEWKAAIEAFNKCKTIYEKLASAFTEEQAVLYNQRVEEISPNIRYCAYNIGDQ 254
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       


Chain D from PDB  Type:PROTEIN  Length:47
                                                                               
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.....................hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 5m73 D 557 KKKGKLPKNYDPKVTPDPERWLPMRERSYYRGRKKGKKKDQIGKGTQ 603
                                   566       576       586       596       


Chain E from PDB  Type:RNA  Length:145
                                                                                                                                                                                 
                 5m73 E 105 gGGUGUCCGCACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGGGAUCGCGCCUA 249
                            |      114       124       134       144       154       164       174       184       194       204       214       224       234       244     
                          105-GTP                                                                                                                                            


Chain F from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhh....................hhhhhhhhhhh....eeeeeeee.......hhh.eeeeee...............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5m73 F  14 RFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKT 117
                                    23        33        43        53        63        73        83        93       103       113    


Chain G from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee..ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m73 G  56 HHHHLEILQIIKESQQQHGLRHGDFQRYRGYCSRRQRRLRKTLNFKMGNRHKFTGKKVTEDLLTDNRYLLLVLMDAERAWSYAMQLKQEANTEPRKRFHLLSRLRKAVKHAEELERLCESNRVDAKTKLEAQAYTAYLSGMLRFEHQEWKAAIEAFNKCKTIYEKLASAFTEEQAVLYNQRVEEISPNIRYCAYNIG 252
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       


Chain H from PDB  Type:PROTEIN  Length:41
                                                                         
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 5m73 H 557 KKKPKNYDPKVPERWLPMRERSYYRGRKKGKKKDQIGKGTQ 603
                              ||   569||     582       592       602 
                            559|    570|                             
                             563     574
   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

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5M73)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M73)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M73)

(-) Gene Ontology  (21, 43)

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  5m73
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  SRP19_HUMAN | P09132
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  SRP68_HUMAN | Q9UHB9
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  SRP72_HUMAN | O76094
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 Related Entries

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

UniProtKB/Swiss-Prot
        SRP19_HUMAN | P09132: 1jid 1mfq 1ry1 2j37 3ktv 4p3e
        SRP68_HUMAN | Q9UHB9: 4p3e 4p3f 5m72 5wrv
        SRP72_HUMAN | O76094: 5m72 5wrv 5wrw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5M73)