Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLR:RAMP2 EXTRACELLULAR DOMAIN HETERODIMER WITH BOUND ADRENOMEDULLIN
 
Authors :  J. Booe, A. Pioszak
Date :  03 Dec 14  (Deposition) - 20 May 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Surface Receptor, Membrane Protein-Hormone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Booe, C. S. Walker, J. Barwell, G. Kuteyi, J. Simms, M. A. Jamaluddin, M. L. Warner, R. M. Bill, P. W. Harris, M. A. Brimble, D. R. Poyner, D. L. Hay, A. A. Pioszak
Structural Basis For Receptor Activity-Modifying Protein-Dependent Selective Peptide Recognition By A G Protein-Coupled Receptor.
Mol. Cell V. 58 1 2015
PubMed-ID: 25982113  |  Reference-DOI: 10.1016/J.MOLCEL.2015.04.018

(-) Compounds

Molecule 1 - MALTOSE TRANSPORTER SUBUNIT, RECEPTOR ACTIVITY-MODIFYING PROTEIN 2, CALCITONIN GENE-RELATED PEPTIDE TYPE 1 RECEPTOR FUSION PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ORIGAMI B DE3
    Expression System Taxid: 562
    Gene: MALE, CE10_4748, RAMP2, CALCRL, CGRPR
    Organism Common: HUMAN
    Organism Scientific: ESCHERICHIA COLI, HOMO SAPIENS
    Organism Taxid: 83333, 9606
    Strain: K12
 
Molecule 2 - ADRENOMEDULLIN
    Chains: B
    Engineered: YES
    Fragment: RESIDUES 119-146
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CGRP TYPE 1 RECEPTOR, CALCITONIN RECEPTOR-LIKE RECEPTOR
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MAL1Ligand/IonMALTOSE
3NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:14 , ASP A:16 , LYS A:17 , TRP A:64 , ALA A:65 , ASP A:67 , ARG A:68 , GLU A:113 , GLU A:155 , PRO A:156 , TYR A:157 , TRP A:342 , HOH A:2315 , HOH A:2326 , HOH A:2362 , HOH A:2368 , HOH A:2489 , HOH A:2495 , HOH A:2591BINDING SITE FOR RESIDUE MAL A 2201
2AC2SOFTWAREASN A:369 , ASP A:1098 , CYS A:1099 , HOH A:2319 , HOH A:2375BINDING SITE FOR RESIDUE EDO A 2202
3AC3SOFTWAREGLY A:15 , LYS A:17 , TYR A:19 , ASP A:298 , LYS A:299 , GLU A:2083 , HOH A:2443BINDING SITE FOR RESIDUE EDO A 2203
4AC4SOFTWAREPRO A:336 , GLN A:337 , GLU A:373 , HOH A:2313BINDING SITE FOR RESIDUE EDO A 2204
5AC5SOFTWARELYS A:181 , ALA A:2044 , GLU A:2047 , HOH A:2553 , HOH A:2666BINDING SITE FOR RESIDUE EDO A 2205
6AC6SOFTWAREASP A:179 , GLU A:2047 , LYS A:2051BINDING SITE FOR RESIDUE EDO A 2206

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:1068 -A:1099
2A:1084 -A:1131
3A:2048 -A:2074
4A:2065 -A:2105
5A:2088 -A:2127

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:1111 -Pro A:1112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RWF)

(-) 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:555
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhh.....eeeee..hhhhhhhh........hhhhhh..hhhhhhhhee..ee..eeeeee..eeeee............hhhhhhhhhhh...eee.....hhhhhhhhhhhh......ee..ee........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhhh..eeee............eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh........ee..ee....ee..ee..eeeeee............eeeeee........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rwf A    3 KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAAEFGGTVKNYETAVQFCWNHYKDQMDPIEKDWCDWAMISRPYSTLRDCLEHFAERFDLGFPNPLAERIIFETHQIHFANCSLVQPTFSIQLGVTRNKIMTAQYECYQKIMQDPIQQAEGVYCNRTWDGWLCWNDVAAGTESMQLCPDYFQDFDPSEKVTKICDQDGNWFRHPASNRTWTNYTQCNV 2129
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 ||   1062      1072      1082      1092      1102      1112      1122      1132      2034      2044      2054      2064      2074      2084      2094      2104      2114      2124     
                                                                                                                                                                                                                                                                                                                                                                                                             374|                                                                                1139|                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                             1055                                                                                 2032                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:19
                                                    
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                4rwf B   35 DKDKDNVAPRSKISPQGYx   53
                                    44        |
                                             53-NH2
   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 4RWF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (113, 145)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:1111 - Pro A:1112   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4rwf
    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
  ADML_HUMAN | P35318
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CALRL_HUMAN | Q16602
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MALE_ECOLI | P0AEX9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RAMP2_HUMAN | O60895
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  ADML_HUMAN | P35318
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CALRL_HUMAN | Q16602
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MALE_ECOLI | P0AEX9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RAMP2_HUMAN | O60895
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ADML_HUMAN | P35318: 2fly 2l7s
        CALRL_HUMAN | Q16602: 3aqf 3n7p 3n7r 3n7s 4rwg
        MALE_ECOLI | P0AEX9: 1a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2d21 2h25 2klf 2mv0 2n44 2n45 2nvu 2obg 2ok2 2r6g 2v93 2vgq 2xz3 2zxt 3a3c 3c4m 3csb 3csg 3d4c 3d4g 3dm0 3ef7 3ehs 3eht 3ehu 3f5f 3g7v 3g7w 3h3g 3h4z 3hpi 3hst 3io4 3io6 3ior 3iot 3iou 3iov 3iow 3j9p 3kjt 3l2j 3lbs 3lc8 3mbp 3mp1 3mp6 3mp8 3mq9 3n94 3o3u 3oai 3osq 3osr 3pgf 3puv 3puw 3pux 3puy 3puz 3pv0 3py7 3q25 3q26 3q27 3q28 3q29 3rlf 3rum 3ser 3ses 3set 3seu 3sev 3sew 3sex 3sey 3vfj 3w15 3wai 3woa 4b3n 4bl8 4bl9 4bla 4blb 4bld 4dxb 4dxc 4edq 4egc 4exk 4fe8 4feb 4fec 4fed 4giz 4gli 4ifp 4ikm 4irl 4jbz 4jkm 4keg 4khz 4ki0 4kv3 4kyc 4kyd 4kye 4log 4mbp 4n4x 4ndz 4o2x 4ogm 4pe2 4qsz 4qvh 4r0y 4rg5 4rwg 4tsm 4wjv 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4wrn 4wth 4wvh 4xa2 4xhs 4xr8 4xzs 4xzv 5aq9 5az6 5az7 5az8 5az9 5aza 5b3w 5b3x 5b3y 5b3z 5c7r 5cbn 5cfv 5dfm 5dis 5e24 5edu 5fio 5fsg 5gru 5gs2 5h7n 5h7q 5hz7 5hzv 5hzw 5i04 5i69 5ihj 5ii5 5iic 5iqz 5jj4 5jst 5jtq 5jtr 5ldf 5t03 5t05 5t0a 5ttd 5wpz 5wq6
        RAMP2_HUMAN | O60895: 2xvt 3aqe 3aqf

(-) Related Entries Specified in the PDB File

4rwg