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(-) Description

Title :  CRYSTAL STRUCTURE OF ERGIC-53/MCFD2, TRIGONAL CALCIUM-BOUND FORM 2
 
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 :  3.05
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (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, E
    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, F
    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 27-146
    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

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CA9Ligand/IonCALCIUM ION
2CL3Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:152 , PHE A:154 , ASN A:156 , ASP A:181binding site for residue CA A 501
02AC2SOFTWAREASP A:155 , ASP A:157 , ASN A:161 , ASN A:162 , ASP A:181binding site for residue CA A 502
03AC3SOFTWARELYS A:53 , GLY A:54 , HIS A:56binding site for residue CL A 503
04AC4SOFTWAREASP B:129 , ASN B:131 , ASP B:133 , TYR B:135 , GLU B:140binding site for residue CA B 501
05AC5SOFTWAREASP B:81 , ASP B:83 , ASN B:85 , LEU B:87 , GLU B:92binding site for residue CA B 502
06AC6SOFTWARELYS C:53 , HIS C:56binding site for residue CL C 502
07AC7SOFTWAREASP D:81 , ASP D:83 , ASN D:85 , LEU D:87 , GLU D:92binding site for residue CA D 501
08AC8SOFTWAREASP D:129 , ASN D:131 , ASP D:133 , TYR D:135 , GLU D:140binding site for residue CA D 502
09AC9SOFTWARELYS E:53 , GLY E:54 , HIS E:56binding site for residue CL E 501
10AD1SOFTWAREASP F:81 , ASP F:83 , ASN F:85 , LEU F:87 , GLU F:92binding site for residue CA F 501
11AD2SOFTWAREASP F:129 , ASN F:131 , ASP F:133 , TYR F:135 , GLU F:140binding site for residue CA F 502

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:190 -A:230
2C:190 -C:230
3E:190 -E:230

(-) Cis Peptide Bonds  (9, 9)

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
7Gly E:54 -Pro E:55
8Ala E:120 -Asp E:121
9Asn E:162 -Pro E:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YGE)

(-) 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhee.............eeeee..ee....eeee......eeeeee........eeeeeeeeee........eeeeeee................eeeeeeee...........eeeeeeee.....hhhhh......eeee.........eeeeeeee..eeeeeee..........eeeeee.........eeeeeee......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yge A  42 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDSFDNDGKKNNPAIVIIGNNGQIHYDHQNDGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLT 268
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       


Chain B from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......eeehhhhhhhh...hhhhhhhhhhhhhhhhh.....eeehhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 4yge B  67 MSPQELQLHYFKMHDYDGNNLLDGLELSTAITHMSEDELINIIDGVLRDDDKNNDGYIDYAEFAKS 144
                                    76        86        96  ||   118       128       138      
                                                           99|                                
                                                           112                                


Chain C from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhee.............eeeee..ee....eeee......eeeeee........eeeeeeeeee........eeeeeee................eeeeeeee.......eeeeeeee.....hhhhhhhhhh.eeee.........eeeeeeee..eeeeeee..........eeeeee.........eeeeeee......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yge C  42 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDSFDKNNPAIVIIGNNGQIHYDHQNDGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLT 268
                                    51        61        71        81        91       101       111       121       131       141       151   ||  165       175       185       195       205       215       225       235       245       255       265   
                                                                                                                                           155|                                                                                                            
                                                                                                                                            160                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......eeehhhhhhhh...hhhhhhhhhhhhhhhhh.....eeehhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 4yge D  67 MSPQELQLHYFKMHDYDGNNLLDGLELSTAITHMSEDELINIIDGVLRDDDKNNDGYIDYAEFAKS 144
                                    76        86        96  ||   118       128       138      
                                                           99|                                
                                                           112                                


Chain E from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhee.............eeeee..ee....eeee......eeeeee........eeeeeeeeee........eeeeeee................eeeeeeee.........eeeeeeee..............eeee.........eeeeeeee..eeeeeee..........eeeeee.........eeeeeee......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yge E  42 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDSFDGKKNNPAIVIIGNNGQIHYDHQGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLT 268
                                    51        61        71        81        91       101       111       121       131       141       151   ||  163       173     ||185       195       205       215       225       235       245       255       265   
                                                                                                                                           155|                  179|                                                                                      
                                                                                                                                            158                   182                                                                                      


Chain F from PDB  Type:PROTEIN  Length:67
                                                                                                   
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......eeehhhhhhhh....hhhhhhhhhhhhhhhhh.....eeehhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 4yge F  67 MSPQELQLHYFKMHDYDGNNLLDGLELSTAITHLMSEDELINIIDGVLRDDDKNNDGYIDYAEFAKS 144
                                    76        86        96  ||   117       127       137       
                                                           99|                                 
                                                           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 4YGE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 46)

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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 4ygb 4ygc 4ygd
        MCFD2_HUMAN | Q8NI22: 2vrg 3a4u 3lcp 3wht 3whu 3wnx 4ygb 4ygc 4ygd

(-) Related Entries Specified in the PDB File

4ygb 4ygc 4ygd