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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN 5T4 (WNT-ACTIVATED INHIBITORY FACTOR 1, TROPHOBLAST GLYCOPROTEIN)
 
Authors :  Y. Zhao, T. Malinauskas, K. Harlos, E. Y. Jones
Date :  21 Jan 14  (Deposition) - 26 Feb 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cell Adhesion, Waif1, Tpbg, Trovax, Cancer, Signaling, Leucine-Rich Repeats, Wnt/Beta-Catenin Signaling Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, T. Malinauskas, K. Harlos, E. Y. Jones
Structural Insights Into The Inhibition Of Wnt Signaling By Cancer Antigen 5T4/Wnt-Activated Inhibitory Factor 1.
Structure V. 22 612 2014
PubMed-ID: 24582434  |  Reference-DOI: 10.1016/J.STR.2014.01.009

(-) Compounds

Molecule 1 - TROPHOBLAST GLYCOPROTEIN
    Atcc: CRL-3022
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S GNTI-
    Expression System Common: HUMAN
    Expression System Plasmid: PURD-5T4/WAIF1ECTO
    Expression System Taxid: 9606
    Expression System Vector: PURD
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN, RESIDUES 60-345
    Organ: KIDNEY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 5T4 ONCOFETAL ANTIGEN, 5T4 ONCOFETAL TROPHOBLAST GLYCOPROTEIN, 5T4 ONCOTROPHOBLAST GLYCOPROTEIN, M6P1,5T4, WNT-ACTIVATED INHIBITORY FACTOR 1
    Tissue: EMBRYONIC KIDNEY

 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  (5, 32)

Asymmetric Unit (5, 32)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5SO414Ligand/IonSULFATE ION
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO48Ligand/IonSULFATE ION
Biological Unit 2 (4, 15)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5SO46Ligand/IonSULFATE ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN B:61 , CYS B:62 , CYS B:68BINDING SITE FOR RESIDUE PEG B1349
02AC2SOFTWAREPHE B:138 , HIS B:140 , LEU B:141BINDING SITE FOR RESIDUE PEG B1350
03AC3SOFTWAREALA A:303 , THR A:307 , LYS A:310 , SER A:339 , LEU A:342 , HOH A:2102BINDING SITE FOR RESIDUE PEG A1351
04AC4SOFTWAREALA B:121 , ARG B:145 , GLU B:177 , SO4 B:1358BINDING SITE FOR RESIDUE PEG B1351
05AC5SOFTWARESER A:126 , ASP A:148 , SER A:150 , HIS A:151 , ASN A:181 , NAG A:1346BINDING SITE FOR RESIDUE GOL A1352
06AC6SOFTWAREASP B:148 , SER B:150 , ASN B:181 , NAG B:1345 , NAG B:1346BINDING SITE FOR RESIDUE GOL B1352
07AC7SOFTWAREASP B:60 , GLN B:61BINDING SITE FOR RESIDUE GOL B1353
08AC8SOFTWAREARG A:214 , HIS A:238 , SER A:262 , HIS A:264 , ARG A:288BINDING SITE FOR RESIDUE SO4 A1353
09AC9SOFTWAREARG A:213 , HIS A:238 , GLU A:261 , HOH A:2105BINDING SITE FOR RESIDUE SO4 A1354
10BC1SOFTWAREPRO A:186 , GLU A:187BINDING SITE FOR RESIDUE SO4 A1355
11BC2SOFTWARESER A:69 , GLU A:70 , ALA A:71 , HOH A:2006BINDING SITE FOR RESIDUE SO4 A1356
12BC3SOFTWAREPRO A:107 , ALA A:108 , ARG A:134BINDING SITE FOR RESIDUE SO4 A1357
13BC4SOFTWARESER B:69 , GLU B:70 , ALA B:71BINDING SITE FOR RESIDUE SO4 B1354
14BC5SOFTWAREARG B:214 , HIS B:238 , SER B:262 , HIS B:264 , ARG B:288BINDING SITE FOR RESIDUE SO4 B1355
15BC6SOFTWAREPRO B:107 , ALA B:108 , ARG B:134 , ARG B:320 , HOH B:2019BINDING SITE FOR RESIDUE SO4 B1356
16BC7SOFTWARESER B:253 , PHE B:254 , ARG B:255BINDING SITE FOR RESIDUE SO4 B1357
17BC8SOFTWARESER A:194 , PHE A:195 , GLU A:196 , HOH A:2050 , HOH A:2061BINDING SITE FOR RESIDUE SO4 A1358
18BC9SOFTWARETHR A:312 , LYS A:318 , HOH A:2095BINDING SITE FOR RESIDUE SO4 A1359
19CC1SOFTWAREARG B:213 , ARG B:214 , HIS B:238 , PEG B:1351BINDING SITE FOR RESIDUE SO4 B1358
20CC2SOFTWAREASN A:79 , ARG B:213 , ARG B:237 , GLU B:261BINDING SITE FOR RESIDUE SO4 A1360
21CC3SOFTWAREHIS B:301 , HOH B:2062BINDING SITE FOR RESIDUE SO4 B1359
22CC4SOFTWARETHR B:307 , LYS B:310 , HOH B:2063 , HOH B:2064 , HOH B:2074BINDING SITE FOR RESIDUE NA B1360
23CC5SOFTWAREASN A:79 , ASN A:81 , HIS B:238 , GLU B:261 , ARG B:288BINDING SITE FOR MONO-SACCHARIDE NAG A1345 BOUND TO ASN A 81
24CC6SOFTWAREPHE A:97 , THR A:99 , ASN A:124 , GLN A:146 , ASP A:148 , GOL A:1352 , HOH A:2038BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1346 THROUGH NAG A1347 BOUND TO ASN A 124
25CC7SOFTWARESER A:219 , HIS A:221 , ASN A:243BINDING SITE FOR MONO-SACCHARIDE NAG A1348 BOUND TO ASN A 243
26CC8SOFTWAREARG A:255 , ASN A:256 , HOH A:2104BINDING SITE FOR MONO-SACCHARIDE NAG A1349 BOUND TO ASN A 256
27CC9SOFTWAREHIS A:238 , GLU A:261 , HIS A:286 , ARG A:288 , HOH A:2074 , HOH A:2083 , ASN B:79 , ASN B:81 , GLN B:102BINDING SITE FOR MONO-SACCHARIDE NAG A1350 BOUND TO ASN B 81
28DC1SOFTWAREPHE B:97 , THR B:99 , ASN B:124 , GLN B:146 , ASP B:148 , GOL B:1352BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1345 THROUGH NAG B1346 BOUND TO ASN B 124
29DC2SOFTWAREHIS B:182 , SER B:219 , HIS B:221 , ASN B:243 , HOH B:2043BINDING SITE FOR MONO-SACCHARIDE NAG B1347 BOUND TO ASN B 243
30DC3SOFTWARELEU B:230 , ALA B:231 , SER B:253 , ARG B:255 , ASN B:256BINDING SITE FOR MONO-SACCHARIDE NAG B1348 BOUND TO ASN B 256

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:62 -A:68
2A:66 -A:77
3A:298 -A:323
4A:300 -A:344
5B:62 -B:68
6B:66 -B:77
7B:298 -B:323
8B:300 -B:344

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:114 -Pro A:115
2Tyr A:325 -Pro A:326
3Arg B:114 -Pro B:115
4Tyr B:325 -Pro B:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 10)

Asymmetric Unit (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.TPBG_HUMAN92-113
 
143-164
 
235-256
 
211-232
 
259-280
 		  10A:92-113
B:92-113
A:143-163
B:143-164
A:235-256
B:235-256
A:211-232
B:211-232
A:259-280
B:259-280
Biological Unit 1 (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.TPBG_HUMAN92-113
 
143-164
 
235-256
 
211-232
 
259-280
 		  5A:92-113
-
A:143-163
-
A:235-256
-
A:211-232
-
A:259-280
-
Biological Unit 2 (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.TPBG_HUMAN92-113
 
143-164
 
235-256
 
211-232
 
259-280
 		  5-
B:92-113
-
B:143-164
-
B:235-256
-
B:211-232
-
B:259-280

(-) Exons   (0, 0)

(no "Exon" information available for 4CNC)

(-) 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:274
 aligned with TPBG_HUMAN | Q13641 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:285
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     
           TPBG_HUMAN    60 DQCPALCECSEAARTVKCVNRNLTEVPTDLPAYVRNLFLTGNQLAVLPAGAFARRPPLAELAALNLSGSRLDEVRAGAFEHLPSLRQLDLSHNPLADLSPFAFSGSNASVSAPSPLVELILNHIVPPEDERQNRSFEGMVVAALLAGRALQGLRRLELASNHFLYLPRDVLAQLPSLRHLDLSNNSLVSLTYVSFRNLTHLESLHLEDNALKVLHNGTLAELQGLPHIRVFLDNNPWVCDCHMADMVTWLKETEVVQGKDRLTCAYPEKMRNRVLLELNSADLDC 344
               SCOP domains d4cnca_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee....eee..................eee......eee...............eee.....eeee............eee.......ee......------.......eee........-----.hhhhhhhhhhhhhhh.....eee.........hhhhhhhh....eee.....................eee.........hhhhhhhhhh....eee.....ee.hhhhhhhhhhhhhh..eehhhhh.eeehhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------LRR  PDB: A:92-113    -----------------------------LRR  PDB: A:143-163   ----------------------------------------------LRR  PDB: A:211-232   --LRR  PDB: A:235-256   --LRR  PDB: A:259-280   ---------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cnc A  60 DQCPALCECSEAARTVKCVNRNLTEVPTDLPAYVRNLFLTGNQLAVLPAGAFARRPPLAELAALNLSGSRLDEVRAGAFEHLPSLRQLDLSHNPLADLSPFAFS------SAPSPLVELILNHIVPPE-----RSFEGMVVAALLAGRALQGLRRLELASNHFLYLPRDVLAQLPSLRHLDLSNNSLVSLTYVSFRNLTHLESLHLEDNALKVLHNGTLAELQGLPHIRVFLDNNPWVCDCHMADMVTWLKETEVVQGKDRLTCAYPEKMRNRVLLELNSADLDC 344
                                    69        79        89        99       109       119       129       139       149       159   |     -|      179       | -   |   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     
                                                                                                                                 163    170              187   193                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with TPBG_HUMAN | Q13641 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:285
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     
           TPBG_HUMAN    60 DQCPALCECSEAARTVKCVNRNLTEVPTDLPAYVRNLFLTGNQLAVLPAGAFARRPPLAELAALNLSGSRLDEVRAGAFEHLPSLRQLDLSHNPLADLSPFAFSGSNASVSAPSPLVELILNHIVPPEDERQNRSFEGMVVAALLAGRALQGLRRLELASNHFLYLPRDVLAQLPSLRHLDLSNNSLVSLTYVSFRNLTHLESLHLEDNALKVLHNGTLAELQGLPHIRVFLDNNPWVCDCHMADMVTWLKETEVVQGKDRLTCAYPEKMRNRVLLELNSADLDC 344
               SCOP domains d4cncb_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee....eee..................eee......eee...............eee.....eeee............eee.......ee...................eee.......-------hhhhhhhhhhhhhhh.....eee.........hhhhhhhh....eee............hhhhh....eee.........hhhhhhhhh.....eee.....ee.hhhhhhhhhhhhhh..eehhhhh.eeehhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------LRR  PDB: B:92-113    -----------------------------LRR  PDB: B:143-164   ----------------------------------------------LRR  PDB: B:211-232   --LRR  PDB: B:235-256   --LRR  PDB: B:259-280   ---------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cnc B  60 DQCPALCECSEAARTVKCVNRNLTEVPTDLPAYVRNLFLTGNQLAVLPAGAFARRPPLAELAALNLSGSRLDEVRAGAFEHLPSLRQLDLSHNPLADLSPFAFSGSNASVSAPSPLVELILNHIVPP-------SFEGMVVAALLAGRALQGLRRLELASNHFLYLPRDVLAQLPSLRHLDLSNNSLVSLTYVSFRNLTHLESLHLEDNALKVLHNGTLAELQGLPHIRVFLDNNPWVCDCHMADMVTWLKETEVVQGKDRLTCAYPEKMRNRVLLELNSADLDC 344
                                    69        79        89        99       109       119       129       139       149       159       169       179      |  -    |  199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     
                                                                                                                                                        186     194
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TPBG_HUMAN | Q13641)
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  4cnc
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  TPBG_HUMAN | Q13641
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 Related Entries

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

UniProtKB/Swiss-Prot
        TPBG_HUMAN | Q13641: 4cnm

(-) Related Entries Specified in the PDB File

4cnm CRYSTAL STRUCTURE OF HUMAN 5T4 (WNT-ACTIVATED INHIBITORY FACTOR 1, TROPHOBLAST GLYCOPROTEIN)