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(-) Description

Title :  CRYSTAL STRUCTURE OF PREFUSION-STABILIZED RSV F VARIANT CAV1 AT PH 5.5
 
Authors :  J. S. Mclellan, M. G. Joyce, G. B. E. Stewart-Jones, M. Sastry, Y. Yang, B. S. Graham, P. D. Kwong
Date :  09 Sep 13  (Deposition) - 20 Nov 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Fusion, Membrane, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Mclellan, M. Chen, M. G. Joyce, M. Sastry, G. B. Stewart-Jones, Y. Yang, B. Zhang, L. Chen, S. Srivatsan, A. Zheng, T. Zhou, K. W. Graepel, A. Kumar, S. Moin, J. C. Boyington, G. Y. Chuang, C. Soto, U. Baxa, A. Q. Bakker, H. Spits, T. Beaumont, Z. Zheng, N. Xia, S. Y. Ko, J. P. Todd, S. Rao, B. S. Graham, P. D. Kwong
Structure-Based Design Of A Fusion Glycoprotein Vaccine For Respiratory Syncytial Virus.
Science V. 342 592 2013
PubMed-ID: 24179220  |  Reference-DOI: 10.1126/SCIENCE.1243283

(-) Compounds

Molecule 1 - FUSION GLYCOPROTEIN F2
    Chains: A, C, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: P(ALPHA)H
    Expression System Strain: FREESTYLE(TM) 293-F
    Expression System Taxid: 9606
    Gene: F
    Mutation: YES
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS A2
    Organism Taxid: 11259
 
Molecule 2 - FUSION GLYCOPROTEIN F1 FUSED WITH FIBRITIN TRIMERIZATION DOMAIN
    Chains: B, D, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: P(ALPHA)H
    Expression System Strain: FREESTYLE(TM) 293-F
    Expression System Taxid: 9606
    Gene: F
    Mutation: YES
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS A2, ENTEROBACTERIA PHAGE T4
    Organism Taxid: 11259, 10665

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1SO414Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE B:137 , ARG B:339 , GLN B:354 , HOH B:777 , HOH B:815 , ARG E:106BINDING SITE FOR RESIDUE SO4 B 601
02AC2SOFTWARESER B:443 , LYS B:445 , LYS B:465 , SER B:466 , HOH B:798BINDING SITE FOR RESIDUE SO4 B 602
03AC3SOFTWARELEU B:273 , ASN B:277 , ARG B:364BINDING SITE FOR RESIDUE SO4 B 603
04AC4SOFTWAREASN B:426 , ARG B:429 , HOH B:840 , SER F:186BINDING SITE FOR RESIDUE SO4 B 604
05AC5SOFTWAREASN B:325 , THR B:326 , LYS B:327 , HOH B:849BINDING SITE FOR RESIDUE SO4 B 605
06AC6SOFTWAREARG A:106 , PHE D:137 , ARG D:339 , GLN D:354 , HOH D:802BINDING SITE FOR RESIDUE SO4 D 601
07AC7SOFTWARESER D:443 , LYS D:445 , GLY D:464 , LYS D:465 , SER D:466BINDING SITE FOR RESIDUE SO4 D 602
08AC8SOFTWARELEU D:273 , ASN D:277 , ARG D:364BINDING SITE FOR RESIDUE SO4 D 603
09AC9SOFTWAREASN D:444 , LYS D:445 , GLY D:446 , LYS D:461 , SO4 D:605BINDING SITE FOR RESIDUE SO4 D 604
10BC1SOFTWAREPRO D:265 , ASN D:426 , LYS D:427 , ASN D:428 , ARG D:429 , SO4 D:604BINDING SITE FOR RESIDUE SO4 D 605
11BC2SOFTWARESER F:443 , LYS F:445 , LYS F:465 , SER F:466 , HOH F:775 , HOH F:830BINDING SITE FOR RESIDUE SO4 F 601
12BC3SOFTWAREPHE F:137 , ARG F:339BINDING SITE FOR RESIDUE SO4 F 602
13BC4SOFTWARELEU F:273 , ARG F:364 , HOH F:801 , HOH F:813BINDING SITE FOR RESIDUE SO4 F 603
14BC5SOFTWAREASN F:444 , LYS F:445 , GLY F:446 , LYS F:461 , HOH F:849BINDING SITE FOR RESIDUE SO4 F 604

(-) SS Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1A:37 -B:439
2A:69 -B:212
3B:313 -B:343
4B:322 -B:333
5B:358 -B:367
6B:382 -B:393
7B:416 -B:422
8C:37 -D:439
9C:69 -D:212
10D:313 -D:343
11D:322 -D:333
12D:358 -D:367
13D:382 -D:393
14D:416 -D:422
15E:37 -F:439
16E:69 -F:212
17F:313 -F:343
18F:322 -F:333
19F:358 -F:367
20F:382 -F:393
21F:416 -F:422

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Lys B:209 -Gln B:210
2Thr B:245 -Pro B:246
3Lys D:209 -Gln D:210
4Thr D:245 -Pro D:246
5Glu D:294 -Glu D:295
6Lys F:209 -Gln F:210
7Thr F:245 -Pro F:246

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MMS)

(-) Sequences/Alignments

Asymmetric/Biological 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:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4mms A  27 NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRA 107
                                    36        46        56        66        76        86        96       106 


Chain B from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....hhhhhhhhhhhh..hhhhhhhhhh.......................hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....................................................................hhhhh...........hhh...hhhhhhhhhh.......................................................................................hhhhhh.............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mms B 137 FLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFI 506
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506


Chain C from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4mms C  27 NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPAT 103
                                    36        46        56        66        76        86        96       


Chain D from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....hhhhhhhhhhhh..hhhhhhhhhh.......................hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....................................................................hhhhh...........hhh...hhhhhhhhhh.......................................................................................hhhhhh.............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mms D 137 FLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFI 506
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506


Chain E from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4mms E  27 NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRA 107
                                    36        46        56        66        76        86        96       106 


Chain F from PDB  Type:PROTEIN  Length:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....hhhhhhhhhhhh..hhhhhhhhhh.......................hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....................................................................hhhhh...........hhh...hhhhhhhhhh.......................................................................................hhhhhh.............hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mms F 137 FLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAF 505
                                   146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496
   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 4MMS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FUS_HRSVA | P03420: 2mdp 3ixt 3kpe 3o41 3o45 3rki 3rrr 3rrt 4ccf 4jhw 4mmq 4mmr 4mmt 4mmu 4mmv 4zyp 5c69 5c6b 5ea3 5ea4 5ea5 5ea6 5ea7 5ea8 5j3d 5k6b 5k6c 5k6f 5k6g 5k6h 5k6i 5toj 5tok 5tpn 5u68 5udc
        WAC_BPT4 | P10104: 1aa0 1avy 1ox3 1rfo 1v1h 1v1i 2bsg 2ibl 2kbl 3a1m 3j2o 4mmq 4mmr 4mmt 4mmu 4mmv 4ncu 4ncv 4ncw

(-) Related Entries Specified in the PDB File

4jhw 4mmq 4mmr 4mmt 4mmu 4mmv