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(-) Description

Title :  CRYSTAL STRUCTURE OF ERGIC-53/MCFD2, MONOCLINIC CALCIUM-FREE FORM
 
Authors :  T. Satoh, M. Nishio, M. Yagi-Utsumi, K. Suzuki, T. Anzai, T. Mizushima, K. Kato
Date :  26 Feb 15  (Deposition) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Beta-Sandwich, Ef-Hand, Cargo Receptor, Calcium Binding, Er, Ergic, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Satoh, M. Nishio, M. Yagi-Utsumi, K. Suzuki, T. Anzai, T. Mizushima Y. Kamiya, K. Kato
Interaction Mode Of Coagulation Factors V And Viii With The Cargo Receptor Mcfd2/Ergic-53 Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN ERGIC-53
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD-III
    Expression System Strain: BL21-CODONPLUS(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 31-269
    Gene: LMAN1, ERGIC53, F5F8D
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ER-GOLGI INTERMEDIATE COMPARTMENT 53 KDA PROTEIN,GP58, INTRACELLULAR MANNOSE-SPECIFIC LECTIN MR60,LECTIN MANNOSE-BINDING 1
 
Molecule 2 - MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-16B
    Expression System Strain: BL21-CODONPLUS(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 67-146
    Gene: MCFD2, SDNSF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEURAL STEM CELL-DERIVED NEURONAL SURVIVAL PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:53 , GLY A:54 , PRO A:55 , HIS A:56 , LEU A:57 , HOH A:427 , LEU B:91 , THR B:95 , HOH B:612binding site for residue GOL A 301
2AC2SOFTWAREASP B:81 , ASP B:83 , ASN B:85 , LEU B:87 , GLU B:92 , HOH B:621binding site for residue CA B 501
3AC3SOFTWAREASP B:129 , ASN B:131 , ASP B:133 , TYR B:135 , GLU B:140 , HOH B:627binding site for residue CA B 502
4AC4SOFTWARELYS C:53 , GLY C:54 , PRO C:55 , HIS C:56 , LEU C:57 , HOH C:453 , LEU D:91 , THR D:95 , HOH D:614binding site for residue GOL C 301
5AC5SOFTWAREASP D:81 , ASP D:83 , ASN D:85 , LEU D:87 , GLU D:92 , HOH D:613binding site for residue CA D 501
6AC6SOFTWAREASP D:129 , ASN D:131 , ASP D:133 , TYR D:135 , GLU D:140 , HOH D:626binding site for residue CA D 502

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:190 -A:230
2C:190 -C:230

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:54 -Pro A:55
2Ala A:120 -Asp A:121
3Asn A:162 -Pro A:163
4Gly C:54 -Pro C:55
5Ala C:120 -Asp C:121
6Asn C:162 -Pro C:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YGB)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhhhee.............eeeee..ee....eeee......eeeeee........eeeeeeeeee........eeeeeee...eeeeeee....eeeeeee.eeeeee.........eeeeeeee..eeeeeee..........eeeeee.........eeeeeee......eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ygb A  42 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAEWNGVGIFFDSFNPAIVIIGNQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLT 268
                                    51        61        71        81        91       101       111       121       145       162       186       196       206       216       226       236       246       256       266  
                                                                                                                 129|       154|     170|                                                                                   
                                                                                                                  144        162      185                                                                                   


Chain B from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......eeehhhhhhhhh..hhhhhhhhhhhhhhhhh.....eeehhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4ygb B  69 PQELQLHYFKMHDYDGNNLLDGLELSTAITLMSEDELINIIDGVLRDDDKNNDGYIDYAEFAK 143
                                    78        88        98|      120       130       140   
                                                        98|                                
                                                        111                                


Chain C from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhhhee.............eeeee..ee....eeee......eeeeee........eeeeeeeeee........eeeeeee...eeeeeee....eeeeeee.eeeeee.........eeeeeeee..eeeeeee..........eeeeee.........eeeeeee......eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ygb C  42 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAEWNGVGIFFDSFNPAIVIIGNQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLT 268
                                    51        61        71        81        91       101       111       121       145       162       186       196       206       216       226       236       246       256       266  
                                                                                                                 129|       154|     170|                                                                                   
                                                                                                                  144        162      185                                                                                   


Chain D from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......eeehhhhhhhhh..hhhhhhhhhhhhhhhhh.....eeehhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4ygb D  69 PQELQLHYFKMHDYDGNNLLDGLELSTAITLMSEDELINIIDGVLRDDDKNNDGYIDYAEFAK 143
                                    78        88        98|      120       130       140   
                                                        98|                                
                                                        111
   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 4YGB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 46)

Asymmetric Unit(hide GO term definitions)

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    Gly C:54 - Pro C:55   [ RasMol ]  
 
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  MCFD2_HUMAN | Q8NI22
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 Related Entries

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

UniProtKB/Swiss-Prot
        LMAN1_HUMAN | P49257: 3a4u 3lcp 3wht 3whu 3wnx 4gkx 4gky 4ygc 4ygd 4yge
        MCFD2_HUMAN | Q8NI22: 2vrg 3a4u 3lcp 3wht 3whu 3wnx 4ygc 4ygd 4yge

(-) Related Entries Specified in the PDB File

4ygc 4ygd 4yge