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(-) Description

Title :  STRUCTURE OF THE GTPASE HETERODIMER OF HUMAN SRP54 AND SRALPHA
 
Authors :  K. Wild, B. Segnitz, I. Sinning
Date :  24 May 16  (Deposition) - 08 Jun 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Co-Translational Protein Targeting, Signal Recognition Particle, Gtpase, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wild, G. Bange, D. Motiejunas, J. Kribelbauer, A. Hendricks, B. Segnitz, R. C. Wade, I. Sinning
Structural Basis For Conserved Regulation And Adaptation Of The Signal Recognition Particle Targeting Complex.
J. Mol. Biol. V. 428 2880 2016
PubMed-ID: 27241309  |  Reference-DOI: 10.1016/J.JMB.2016.05.015

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SRP54
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE C-TERMINAL M DOMAIN WAS DEGRADED DURING CRYSTALLIZATION
    Synonym: SRP54
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SRPRA, SRPR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE N-TERMINAL LONGIN DOMAIN (SRX) AND THE LINKER TO THE NG DOMAIN ARE DEGRADED DURING CRYSTALLIZATION
    Synonym: SR-ALPHA,DOCKING PROTEIN ALPHA,DP-ALPHA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2GNP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL4Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION
5SO49Ligand/IonSULFATE ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL2Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5SO45Ligand/IonSULFATE ION
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL2Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5SO44Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:154 , HIS A:278 , ILE A:279 , AMP A:505 , GOL B:707binding site for residue SO4 A 501
02AC2SOFTWAREGLN A:110 , GLY A:111 , SER A:112 , GLY A:113 , LYS A:114 , THR A:115 , THR A:116 , LYS A:120 , ASP A:138 , ARG A:141 , GLN A:147 , GLY A:193 , LYS A:249 , ASP A:251 , GLY A:274 , THR A:275 , GLY A:276 , GLU A:277 , MG A:503 , HOH A:603 , HOH A:609 , ASN B:427 , ARG B:458 , GNP B:705binding site for residue GNP A 502
03AC3SOFTWARETHR A:115 , GNP A:502 , HOH A:601 , HOH A:609 , HOH A:610binding site for residue MG A 503
04AC4SOFTWARELYS A:286 , THR A:287 , GLN A:288binding site for residue GOL A 504
05AC5SOFTWAREGLU A:277 , HIS A:278 , SO4 A:501 , HOH A:607 , HOH A:618 , HOH A:619 , PHE B:457 , GLY B:523 , LEU B:531 , GOL B:707binding site for residue AMP A 505
06AC6SOFTWAREARG B:466 , ARG B:470 , HOH B:803binding site for residue SO4 B 701
07AC7SOFTWARELYS B:496 , ASP B:497binding site for residue SO4 B 702
08AC8SOFTWARETHR B:467 , ARG B:470 , HOH B:827binding site for residue SO4 B 703
09AC9SOFTWAREASP B:497 , MET B:503 , LYS B:537 , VAL B:541binding site for residue SO4 B 704
10AD1SOFTWAREGLN A:110 , ARG A:141 , GNP A:502 , ASN B:427 , GLY B:428 , VAL B:429 , GLY B:430 , LYS B:431 , SER B:432 , THR B:433 , ASN B:434 , LYS B:437 , ARG B:458 , GLN B:464 , LYS B:589 , ASP B:591 , GLY B:615 , THR B:616 , GLY B:617 , GLN B:618 , MG B:706 , HOH B:804 , HOH B:805 , HOH B:809 , HOH B:816 , HOH B:819binding site for residue GNP B 705
11AD2SOFTWARESER B:432 , ASP B:520 , GNP B:705 , HOH B:804 , HOH B:805 , HOH B:819binding site for residue MG B 706
12AD3SOFTWARELYS A:154 , SO4 A:501 , AMP A:505 , PHE B:457 , ALA B:459 , HOH B:822binding site for residue GOL B 707
13AD4SOFTWARELYS C:47 , LYS D:596binding site for residue SO4 C 501
14AD5SOFTWARELYS C:154 , HIS C:278 , ILE C:279 , GOL D:705binding site for residue SO4 C 502
15AD6SOFTWAREGLN C:110 , GLY C:111 , SER C:112 , GLY C:113 , LYS C:114 , THR C:115 , THR C:116 , LYS C:120 , ASP C:138 , ARG C:141 , GLN C:147 , GLY C:193 , LYS C:249 , ASP C:251 , GLY C:274 , THR C:275 , GLY C:276 , GLU C:277 , MG C:504 , HOH C:601 , HOH C:602 , HOH C:603 , HOH C:606 , HOH C:607 , HOH C:611 , ASN D:427 , ARG D:458 , GNP D:703 , HOH D:819binding site for residue GNP C 503
16AD7SOFTWARETHR C:115 , GNP C:503 , HOH C:601 , HOH C:602 , HOH C:603binding site for residue MG C 504
17AD8SOFTWAREHIS C:253 , LYS D:565binding site for residue GOL C 505
18AD9SOFTWAREGLU C:277 , HIS C:278 , HOH C:605 , HOH C:609 , PHE D:457 , GLY D:523 , LEU D:531 , GOL D:705binding site for residue AMP C 506
19AE1SOFTWAREARG D:470 , ARG D:471binding site for residue SO4 D 701
20AE2SOFTWAREASP D:497binding site for residue SO4 D 702
21AE3SOFTWAREGLN C:110 , ARG C:141 , GNP C:503 , ASN D:427 , GLY D:428 , VAL D:429 , GLY D:430 , LYS D:431 , SER D:432 , THR D:433 , ASN D:434 , LYS D:437 , ARG D:458 , GLN D:464 , GLY D:523 , LYS D:589 , ASP D:591 , GLY D:615 , THR D:616 , GLY D:617 , GLN D:618 , MG D:704 , HOH D:802 , HOH D:803 , HOH D:804 , HOH D:812binding site for residue GNP D 703
22AE4SOFTWARESER D:432 , ARG D:458 , GNP D:703 , HOH D:804 , HOH D:808 , HOH D:812binding site for residue MG D 704
23AE5SOFTWAREASN C:151 , LYS C:154 , SO4 C:502 , AMP C:506 , HOH C:606 , PHE D:457 , ARG D:458 , ALA D:459 , HOH D:825binding site for residue GOL D 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L3Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L3Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L3Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L3Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5L3Q)

(-) 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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhh..eeeee.......eee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l3q A  24 NEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAIDNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFKNENFEIIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEAQAKAFKDKVDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISKLLG 296
                                    33        43        53       |71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
                                                                61|                                                                                                                                                                                                                                  
                                                                 70                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhh..........eeeeehhhhh....hhhhhhhhhh...eeeee.......ee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l3q B 332 SLSREDMESVLDKMRDHLIAKNVAADIAVQLCESVANKLEGKVMGTFSTVTSTVKQALQESLVQILQPQRRVDMLRDIMDAQRRQRPYVVTFCGVNGVGKSTNLAKISFWLLENGFSVLIAACDTFRAGAVEQLRTHTRRLSALHPPEKHGGRTMVQLFEKGYGKDAAGIAMEAIAFARNQGFDVVLVDTAGRMQDNAPLMTALAKLITVNTPDLVLFVGEALVGNEAVDQLVKFNRALADHSMAQTPRLIDGIVLTKFDTIDDKVGAAISMTYITSKPIVFVGTGQTYCDLRSLNAKAVVAALMKA 638
                                   341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       


Chain C from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.............eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh...eeeee.........hhhhhhhhhh..eeeee.......eee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l3q C  24 NEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAIDNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFKNENFEIIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEAQAKAFKDKVDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISKLLG 296
                                    33        43        53       |71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
                                                                61|                                                                                                                                                                                                                                  
                                                                 70                                                                                                                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhh..........eeeeehhhhh....hhhhhhhhhh...eeeee.......ee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l3q D 332 SLSREDMESVLDKMRDHLIAKNVAADIAVQLCESVANKLEGKVMGTFSTVTSTVKQALQESLVQILQPQRRVDMLRDIMDAQRRQRPYVVTFCGVNGVGKSTNLAKISFWLLENGFSVLIAACDTFRAGAVEQLRTHTRRLSALHPPEKHGGRTMVQLFEKGYGKDAAGIAMEAIAFARNQGFDVVLVDTAGRMQDNAPLMTALAKLITVNTPDLVLFVGEALVGNEAVDQLVKFNRALADHSMAQTPRLIDGIVLTKFDTIDDKVGAAISMTYITSKPIVFVGTGQTYCDLRSLNAKAVVAALMKA 638
                                   341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631
   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 5L3Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L3Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L3Q)

(-) Gene Ontology  (34, 38)

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  5l3q
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  SRP54_HUMAN | P61011
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  SRPRA_HUMAN | P08240
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 Related Entries

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

UniProtKB/Swiss-Prot
        SRP54_HUMAN | P61011: 1mfq 1qb2
        SRPRA_HUMAN | P08240: 2fh5 2go5

(-) Related Entries Specified in the PDB File

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