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(-) Description

Title :  MOUSE SEMAPHORIN 3A, DOMAINS SEMA-PSI-IG
 
Authors :  B. J. C. Janssen, T. Malinauskas, C. Siebold, E. Y. Jones
Date :  06 Sep 12  (Deposition) - 17 Oct 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sema, Multi-Domain, Cell-Cell Signaling, Plexin, Glycosilated, Extracellular, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. C. Janssen, T. Malinauskas, G. A. Weir, M. Z. Cader, C. Siebold, E. Y. Jones
Neuropilins Lock Secreted Semaphorins Onto Plexins In A Ternary Signaling Complex.
Nat. Struct. Mol. Biol. V. 19 1293 2012
PubMed-ID: 23104057  |  Reference-DOI: 10.1038/NSMB.2416

(-) Compounds

Molecule 1 - SEMAPHORIN-3A
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 21-675
    Gene: SEMA3A, SEMAD, SEMD
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: SEMAPHORIN III, SEMA III, SEMAPHORIN-D, SEMA D

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 67)

Asymmetric/Biological Unit (6, 67)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BMA2Ligand/IonBETA-D-MANNOSE
3CA5Ligand/IonCALCIUM ION
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
6UNK49Mod. Amino Acid

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:310 , GLN A:433BINDING SITE FOR RESIDUE CA A 807
02AC2SOFTWAREGLU A:122BINDING SITE FOR RESIDUE CA A 808
03AC3SOFTWARELEU A:51 , SER A:54 , TYR A:57BINDING SITE FOR RESIDUE CA A 809
04AC4SOFTWAREASN A:44 , LYS A:460 , GLU A:478 , PRO A:513BINDING SITE FOR RESIDUE ACT A 810
05AC5SOFTWAREASP B:310 , GLN B:433BINDING SITE FOR RESIDUE CA B 801
06AC6SOFTWAREGLU B:122BINDING SITE FOR RESIDUE CA B 802
07AC7SOFTWAREASN B:125 , THR B:127 , HIS B:128 , TYR B:143BINDING SITE FOR RESIDUE NAG B 807
08AC8SOFTWAREASN B:44 , LYS B:460 , GLU B:478 , PRO B:513BINDING SITE FOR RESIDUE ACT B 808
09AC9SOFTWAREASN A:53 , HIS A:76 , LYS A:90 , VAL A:92BINDING SITE FOR LINKED RESIDUES A 801 TO 804
10BC1SOFTWARETYR A:124 , ASN A:125 , THR A:127 , HIS A:128 , GLN A:158BINDING SITE FOR LINKED RESIDUES A 805 TO 806
11BC2SOFTWAREASN B:53 , HIS B:76 , LYS B:90 , VAL B:92BINDING SITE FOR LINKED RESIDUES B 803 TO 806

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:103 -A:114
2A:132 -A:141
3A:269 -A:381
4A:293 -A:341
5A:517 -A:535
6A:524 -A:567
7A:527 -A:542
8B:103 -B:114
9B:132 -B:141
10B:269 -B:381
11B:293 -B:341
12B:517 -B:535
13B:524 -B:567
14B:527 -B:542

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:150 -Glu A:151
2Tyr A:375 -Pro A:376
3Tyr B:375 -Pro B:376
4Pro B:547 -Thr B:548

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 4GZ8)

(-) 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:557
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhh...eee..........eeeee....eeeee...eeeeee......eeeee...hhhhhhhhhhh...........eeeeeeee..eeeeee......eeeeee..........ee.....ee.............eeeee..eeeeeee.......eeeeee......ee............eeeeeeee.........eeeeeeeee.........eeeeeeeee.................eeeee..ee.......ee..eeeeeeee........eeeeeee........eeeeeeehhhhhhhhhh..ee........ee...........................hhhhhhh............hhhhh..eee......eeeeeeeeee....eeeeeeeee...eeeeeeee..eeeeeeeee.........eeeee....eeeee....eeeee..hhhhh..hhhhhhhh....ee......ee............................eee..eeee...eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gz8 A  27 NNVPRLKLSYKEMLESNNVITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIKDFQKIVWPVSYTRRDECKWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDGELYSGTAADFMGRDFAIFRTLGHHHPIRTEQHDSRWLNDPRFISAHLIPESDNPEDDKVYFFFRENAIDGHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRRVFLGPYAHRDGPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRPIMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPLEEVLLEEMTVFREPTTISAMELSTKQQQLYIGSTAGVAQLPLHRCDIYGKACAECCLARDPYCAWDGSSCSRYFPTRAQDIRNGDPLTHCSDxxxxxxxxxxxxxxxxxxxxxxxxxx 666
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       473       483       493       503       513       523       533       543   ||  558       568|||||||606|||||||656|||||||
                                                                                                                                                                                                                                                             254|                                                                                                                                                                                                              465|                                                                        547|             569||||||606-UNK||655-UNK||||
                                                                                                                                                                                                                                                              256                                                                                                                                                                                                               472                                                                         553              598-UNK||607-UNK||656-UNK|||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              599-UNK||608-UNK||660-UNK||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               600-UNK| 609-UNK| 661-UNK|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                601-UNK  650-UNK  662-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 602-UNK  651-UNK  663-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  603-UNK  652-UNK  664-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   604-UNK  653-UNK  665-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    605-UNK  654-UNK  666-UNK


Chain B from PDB  Type:PROTEIN  Length:555
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeehhhhhhhh...eee..........eeeee....eeeee...eeeeee......eeeee...hhhhhhhhhhh...........eeeeeeee..eeeeee......eeeeee..........ee.....ee.............eeeee..eeeeeee.......eeeeee......ee............eeeeeeee.........eeeeeeeee.......eeeeeeeee.................eeeee..ee.......ee..eeeeeeee........eeeeeee........eeeeeeehhhhhhhhhh..ee........ee...........................hhhhhhh............hhhhh..eee......eeeeeeeeee....eeeeeeeee...eeeeeeee...eeeeeeeee.........eeeee....eeeee....eeeee..hhhhh..hhhhhhhh....ee......ee...................................ee....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gz8 B  26 KNNVPRLKLSYKEMLESNNVITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIKDFQKIVWPVSYTRRDECKWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDGELYSGTAADFMGRDFAIFRTLGHHHPIRTEQHDSRWLNDPRFISAHLIPESDNPEDDKVYFFFRENAIDSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRRVFLGPYAHRDGPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRPIMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPKLEEVLLEEMTVFREPTTISAMELSTKQQQLYIGSTAGVAQLPLHRCDIYGKACAECCLARDPYCAWDGSSCSRYFPTTRAQDIRNGDPLTHCSDxxxxxxxxxxxxxxxxxxxxxxx 665
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       473       483       493       503       513       523       533       543    || 557       567 ||||||606|||||||654|||||
                                                                                                                                                                                                                                                             253|                                                                                                                                                                                                              466|                                                                         548|             569||||||607-UNK||654-UNK|
                                                                                                                                                                                                                                                              257                                                                                                                                                                                                               472                                                                          553              599-UNK||608-UNK||661-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               600-UNK||609-UNK||662-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                601-UNK| 610-UNK| 663-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 602-UNK  649-UNK  664-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  603-UNK  650-UNK  665-UNK
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   604-UNK  651-UNK    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    605-UNK  652-UNK   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     606-UNK  653-UNK
   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 4GZ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GZ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GZ8)

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        SEM3A_MOUSE | O08665: 1q47 4gza

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