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(-) Description

Title :  CRYSTAL STRUCTURE OF VOLTAGE SENSING DOMAIN OF CI-VSP WITH FRAGMENT ANTIBODY (R217E, 2.8 A)
 
Authors :  Q. Li
Date :  20 Jul 12  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  H,L,S
Keywords :  Membrane Protein, Alpha Helix, Fragment Antibody, Voltage Sensing Domain, Sensing Voltage (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Li, M. Paduch, S. Wanderling, R. E. Hulse, S. Koide, A. Kosiakoff, E. Perozo
Structural Rearrangement In Voltage Sensing Domain Of Ci-Vs
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FRAGMENT ANTIBODY HEAVY CHAIN
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHAGEMID CODING FOR BOTH HEAVY CHAIN AND LIGHT CHAIN OF THE FRAGMENT ANTIBODY
    Expression System Strain55244
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - FRAGMENT ANTIBODY LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHAGEMID CODING FOR BOTH HEAVY CHAIN AND LIGHT CHAIN OF THE FRAGMENT ANTIBODY
    Expression System Strain55244
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - VOLTAGE-SENSOR CONTAINING PHOSPHATASE
    ChainsS
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE32 WITH SEQUENCE ENCODING FOR CI-VSD
    Expression System StrainXL10-GOLD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCI-VSP
    MutationYES
    Organism CommonSEA VASE,YELLOW SEA SQUIRT
    Organism ScientificCIONA INTESTINALIS
    Organism Taxid7719

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HLS

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2LDA1Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO L:59 , ARG L:61BINDING SITE FOR RESIDUE CL L 301
2AC2SOFTWAREHOH H:302 , HOH H:303 , HOH H:304 , HOH H:305 , ASP L:167 , HOH L:410BINDING SITE FOR RESIDUE MG L 302
3AC3SOFTWARESER L:28 , PHE L:92 , TYR L:93 , VAL S:196 , PHE S:199 , ASP S:204BINDING SITE FOR RESIDUE LDA S 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:146 -H:202
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Phe H:152 -Pro H:153
2Glu H:154 -Pro H:155
3Ser L:7 -Pro L:8
4Trp L:94 -Pro L:95
5Tyr L:140 -Pro L:141
6Leu S:116 -Gly S:117
7Asp S:204 -Glu S:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4G7Y)

(-) 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 H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee......eeeeeeehhhheeee.......eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee...eeeeeeeeeee.......ee.........ee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g7y H   1 EVQLVESGGGLVQPGGSLRLSCAASGFNVSSSSIHWVRQAPGKGLEWVASISSYYGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSYSWSYAIDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    147       157       167       177       187       197       207       217  
                                                                                                                                                             132|                                                                               
                                                                                                                                                              140                                                                               

Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d4g7yl1 L:1-107 automated matches                                                                          d4g7yl2 L:108-211 automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g7y L   1 DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYFYWPITFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQAGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 

Chain S from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g7y S 104 RVQFRVRAVIDHLGMRVFGVFLIFLDIILMIIDLSLPGKSESSQSFYDGMALALSCYFMLDLGLRIFAYGPKNFFTNPWEVADGLIIVVTFVVTIFYTVLDEYVQETGADGLGELVVLARLLRVVRLARIF 234
                                   113       123       133       143       153       163       173       183       193       203       213       223       233 

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G7Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G7Y)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp S:204 - Glu S:205   [ RasMol ]  
    Glu H:154 - Pro H:155   [ RasMol ]  
    Leu S:116 - Gly S:117   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp L:94 - Pro L:95   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q4W8A1_CIOIN | Q4W8A14g7v 4g80
UniProtKB/TrEMBL
        Q4W8A1_CIOIN | Q4W8A13awe 3awf 3awg 3v0d 3v0e 3v0f 3v0g 3v0h 3v0i 3v0j

(-) Related Entries Specified in the PDB File

4g7v 4g80