Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF LAMPREY VARIABLE LYMPHOCYTE RECEPTOR 2913 ECTODOMAIN
 
Authors :  B. W. Han, B. R. Herrin, J. Choe, M. D. Cooper, I. A. Wilson
Date :  13 Sep 07  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Adaptive Immunity, Vlr, Leucine-Rich Repeat, Lrr, Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Han, B. R. Herrin, G. M. Morris, J. Choe, M. D. Cooper, I. A. Wilson
Crystal Structure Of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - VARIABLE LYMPHOCYTE RECEPTOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PBAC6
    Expression System Strain: HI 5
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRAL EXPRESSION
    Fragment: EXTRACELLULAR DOMAIN
    Organism Common: SEA LAMPREY
    Organism Scientific: PETROMYZON MARINUS
    Organism Taxid: 7757

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2R9U)

(-) Sites  (0, 0)

(no "Site" information available for 2R9U)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:22 -A:28
2A:26 -A:35
3A:135 -A:170
4A:137 -A:190
5B:22 -B:28
6B:26 -B:35
7B:135 -B:170
8B:137 -B:190
9C:22 -C:28
10C:26 -C:35
11C:135 -C:170
12C:137 -C:190
13D:22 -D:28
14D:26 -D:35
15D:135 -D:170
16D:137 -D:190

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R9U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R9U)

(-) Exons   (0, 0)

(no "Exon" information available for 2R9U)

(-) 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:174
 aligned with Q6E4B4_PETMA | Q6E4B4 from UniProtKB/TrEMBL  Length:273

    Alignment length:174
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
         Q6E4B4_PETMA    17 QSAVACPSQCSCDQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLRNWVADHTSIVMRWDGKAVNDPDSAKCAGTNTPVRAVTEASTSPSKC 190
               SCOP domains d2r9ua_ A: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee...eee..................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhh...eeee...eee.hhhh.......hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r9u A  17 HHSAGCPSQCSCDQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLRNWVADHTSIVMRWDGKAVNDPDSAKCAGTNTPVRAVTEASTSPSKC 190
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with Q6E4B4_PETMA | Q6E4B4 from UniProtKB/TrEMBL  Length:273

    Alignment length:174
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
         Q6E4B4_PETMA    17 QSAVACPSQCSCDQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLRNWVADHTSIVMRWDGKAVNDPDSAKCAGTNTPVRAVTEASTSPSKC 190
               SCOP domains d2r9ub_ B: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee...eee..................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhhhhh.eee...eee............hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r9u B  17 HHSAGCPSQCSCDQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLRNWVADHTSIVMRWDGKAVNDPDSAKCAGTNTPVRAVTEASTSPSKC 190
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    


Chain C from PDB  Type:PROTEIN  Length:174
 aligned with Q6E4B4_PETMA | Q6E4B4 from UniProtKB/TrEMBL  Length:273

    Alignment length:174
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
         Q6E4B4_PETMA    17 QSAVACPSQCSCDQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLRNWVADHTSIVMRWDGKAVNDPDSAKCAGTNTPVRAVTEASTSPSKC 190
               SCOP domains d2r9uc_ C: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee...eee..................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhh...eeee...eee.hhhh.......hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r9u C  17 HHSAGCPSQCSCDQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLRNWVADHTSIVMRWDGKAVNDPDSAKCAGTNTPVRAVTEASTSPSKC 190
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    


Chain D from PDB  Type:PROTEIN  Length:174
 aligned with Q6E4B4_PETMA | Q6E4B4 from UniProtKB/TrEMBL  Length:273

    Alignment length:174
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
         Q6E4B4_PETMA    17 QSAVACPSQCSCDQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLRNWVADHTSIVMRWDGKAVNDPDSAKCAGTNTPVRAVTEASTSPSKC 190
               SCOP domains d2r9ud_ D: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------------------------LRR_8-2r9uD01 D:78-132                                 ---DUF3439-2r9uD09 D:136-190                               Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------LRR_8-2r9uD02 D:78-132                                 ---DUF3439-2r9uD10 D:136-190                               Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------LRR_8-2r9uD03 D:78-132                                 ---DUF3439-2r9uD11 D:136-190                               Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------LRR_8-2r9uD04 D:78-132                                 ---DUF3439-2r9uD12 D:136-190                               Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------LRR_8-2r9uD05 D:78-132                                 ---------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------LRR_8-2r9uD06 D:78-132                                 ---------------------------------------------------------- Pfam domains (6)
           Pfam domains (7) -------------------------------------------------------------LRR_8-2r9uD07 D:78-132                                 ---------------------------------------------------------- Pfam domains (7)
           Pfam domains (8) -------------------------------------------------------------LRR_8-2r9uD08 D:78-132                                 ---------------------------------------------------------- Pfam domains (8)
         Sec.struct. author ..........ee...eee..................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhh...eeee...eee.hhhh.......hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r9u D  17 HHSAGCPSQCSCDQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWDCECRDIMYLRNWVADHTSIVMRWDGKAVNDPDSAKCAGTNTPVRAVTEASTSPSKC 190
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R9U)

(-) Pfam Domains  (2, 12)

Asymmetric Unit
(-)
Clan: LRR (77)
(-)
Family: LRR_8 (41)
(-)
Petromyzon marinus (Sea lamprey) (3)
1aLRR_8-2r9uD01D:78-132
1bLRR_8-2r9uD02D:78-132
1cLRR_8-2r9uD03D:78-132
1dLRR_8-2r9uD04D:78-132
1eLRR_8-2r9uD05D:78-132
1fLRR_8-2r9uD06D:78-132
1gLRR_8-2r9uD07D:78-132
1hLRR_8-2r9uD08D:78-132
(-)
Clan: no clan defined [family: DUF3439] (3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2R9U)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2r9u)
 
  Sites
(no "Sites" information available for 2r9u)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r9u)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2r9u
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q6E4B4_PETMA | Q6E4B4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q6E4B4_PETMA | Q6E4B4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2R9U)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2R9U)