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(-) Description

Title :  CRYSTAL STRUCTURE OF SCARB2 IN NEURAL CONDITION (PH7.5)
 
Authors :  M. H. Dang, X. X. Wang, Z. H. Rao
Date :  29 Jun 14  (Deposition) - 08 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lipid Binding Tunnel, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Dang, X. Wang, Q. Wang, Y. Wang, J. Lin, Y. Sun, X. Li, L. Zhang, Z. Lou, J. Wang, Z. Rao
Molecular Mechanism Of Scarb2-Mediated Attachment And Uncoating Of Ev71
Protein Cell V. 5 692 2014
PubMed-ID: 24986489  |  Reference-DOI: 10.1007/S13238-014-0087-3

(-) Compounds

Molecule 1 - SCAVENGER RECEPTOR CLASS B MEMBER 2
    ChainsA, B
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBAC_BEE
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentECTODOMAIN, UNP RESIDUES 37-430
    GeneSCARB2, CD36L2, LIMP2, LIMPII
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLYSOSOME MEMBRANE PROTEIN 2, 85 KDA LYSOSOMAL MEMBRANE SIALOGLYCOPROTEIN, LGP85, CD36 ANTIGEN-LIKE 2, LYSOSOME MEMBRANE PROTEIN II, LIMP II

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 35)

Asymmetric Unit (3, 35)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2MAN6Ligand/IonALPHA-D-MANNOSE
3NAG23Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 21)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:68 , VAL A:86 , LEU A:132 , ARG A:134 , THR A:170 , GLU B:79binding site for Poly-Saccharide residues NAG A 501 through MAN A 505 bound to ASN A 68
02AC2SOFTWARETYR A:117 , TRP A:178 , ASN A:206binding site for Poly-Saccharide residues NAG A 506 through NAG A 507 bound to ASN A 206
03AC3SOFTWARELEU A:216 , ASP A:220 , SER A:221 , ASN A:224binding site for Mono-Saccharide NAG A 508 bound to ASN A 224
04AC4SOFTWARELYS A:244 , CYS A:245 , MET A:247 , ASN A:249 , TYR A:267 , SER A:276 , ASP A:307binding site for Poly-Saccharide residues NAG A 509 through BMA A 511 bound to ASN A 249
05AC5SOFTWAREASN A:304 , CYS A:318 , LEU A:319 , ARG A:348binding site for Poly-Saccharide residues NAG A 512 through NAG A 513 bound to ASN A 304
06AC6SOFTWAREASP A:122 , VAL A:149 , ILE A:313 , LEU A:319 , ASN A:325 , ILE A:328binding site for Poly-Saccharide residues NAG A 514 through MAN A 517 bound to ASN A 325
07AC7SOFTWAREGLN A:63 , TYR A:65 , ASP A:362 , ARG A:382 , ASN A:412binding site for Poly-Saccharide residues NAG A 518 through MAN A 521 bound to ASN A 412
08AC8SOFTWAREGLU A:79 , ASN B:68 , LEU B:132 , ARG B:134 , THR B:170binding site for Poly-Saccharide residues NAG B 501 through MAN B 504 bound to ASN B 68
09AC9SOFTWARETYR B:117 , TRP B:178 , ASN B:206binding site for Poly-Saccharide residues NAG B 505 through NAG B 506 bound to ASN B 206
10AD1SOFTWARELEU B:216 , ASP B:220 , SER B:221 , ASN B:224binding site for Mono-Saccharide NAG B 507 bound to ASN B 224
11AD2SOFTWARELYS B:244 , CYS B:245 , MET B:247 , ASN B:249 , TYR B:267 , SER B:276binding site for Mono-Saccharide NAG B 508 bound to ASN B 249
12AD3SOFTWAREVAL B:149 , LEU B:319 , ASN B:325 , SER B:327 , ILE B:328 , TYR B:388binding site for Poly-Saccharide residues NAG B 509 through NAG B 510 bound to ASN B 325
13AD4SOFTWAREGLN B:63 , TYR B:65 , GLU B:85 , ASP B:362 , ARG B:382 , TYR B:410 , ASN B:412 , SER B:414binding site for Poly-Saccharide residues NAG B 511 through MAN B 514 bound to ASN B 412

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:274 -A:329
2A:312 -A:318
3B:274 -B:329
4B:312 -B:318

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:87 -Pro A:88
2Ile A:313 -Pro A:314
3Gly B:87 -Pro B:88
4Ile B:313 -Pro B:314

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TW2)

(-) Exons   (0, 0)

(no "Exon" information available for 4TW2)

(-) 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:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhh....eeeeeeeeee.hhhhhhh.....eeeeeeeeeeeeeeeeeeeeehhh.eeeeeeeeeeeee...........eeeeehhhhhhhhhhhhh.......hhhhhhh....eeeeehhhhhhheehhhhhhhhhhh.....ee.............eeee....hhhhh.eeeee..................................eee.hhhhh..eeeeeeeeeee..eeeeeee........hhhhhhhh..........eee.........eeee.hhhh..hhhhhhhh.....hhhhhh.eeeee....eeeeeeeeeeeeeee.....hhhhh....eeeeeeeeeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tw2 A  37 IEKKIVLRNGTEAFDSWEKPPLPVYTQFYFFNVTNPEEILRGETPRVEEVGPYTYRELRNKANIQFGDNGTTISAVSNKAYVFERDQSVGDPKIDLIRTLNIPVLTVIEWSQVHFLREIIEAMLKAYQQKLFVTHTVDELLWGYKDEILSLIHVFRPDISPYFGLFYEKNGTNDGDYVFLTGEDSYLNFTKIVEWNGKTSLDWWITDKCNMINGTDGDSFHPLITKDEVLYVFPSDFCRSVYITFSDYESVQGLPAFRYKVPAEILANTSDNAGFCIPEGNCLGSGVLNVSICKNGAPIIMSFPHFYQADERFVSAIEGMHPNQEDHETFVDINPLTGIILKAAKRFQINIYVKKLDDFVETGDIRTMVFPVMYLNESVHIDKETASRLKSMIN 430
                                    46        56        66        76        86        96       106       116       126       136       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    

Chain B from PDB  Type:PROTEIN  Length:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhh....eeeeeeeeee.hhhhhhh.....eeeeeeeeeeeeeeeeeeeeehhh.eeeeeeeeeeeee...........eeeeehhhhhhhhhhhhh.......hhhhhhh....eeeeehhhhhhheehhhhhhhhhhh.....ee........eeeeeeeee..........eeeee..................................eee.hhhhh..eeeeeeeeeee..eeeeeee........hhhhhhhh..........eee.........eeee.hhhh..hhhhhhhh.....hhhhhh.eeeee....eeeeeeeeeeeeeee.....hhhhh....eeeeeeeeeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tw2 B  37 IEKKIVLRNGTEAFDSWEKPPLPVYTQFYFFNVTNPEEILRGETPRVEEVGPYTYRELRNKANIQFGDNGTTISAVSNKAYVFERDQSVGDPKIDLIRTLNIPVLTVIEWSQVHFLREIIEAMLKAYQQKLFVTHTVDELLWGYKDEILSLIHVFRPDISPYFGLFYEKNGTNDGDYVFLTGEDSYLNFTKIVEWNGKTSLDWWITDKCNMINGTDGDSFHPLITKDEVLYVFPSDFCRSVYITFSDYESVQGLPAFRYKVPAEILANTSDNAGFCIPEGNCLGSGVLNVSICKNGAPIIMSFPHFYQADERFVSAIEGMHPNQEDHETFVDINPLTGIILKAAKRFQINIYVKKLDDFVETGDIRTMVFPVMYLNESVHIDKETASRLKSMIN 430
                                    46        56        66        76        86        96       106       116       126       136       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    

   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 4TW2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TW2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TW2)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        SCRB2_HUMAN | Q141084f7b 4q4b 4q4f 4tvz 4tw0

(-) Related Entries Specified in the PDB File

4tvz 4tw0