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(-) Description

Title :  THE CRYSTAL STRUCTURES OF HOLO-WT HUMAN CELLULAR RETINOL BINDING PROTEIN II (HCRBPII) BOUND TO RETINAL
 
Authors :  Z. Nossoni, Z. Assar, I. Yapici, M. Nosrati, W. Wang, T. Berbasova, C. Va B. Borhan, H. Geiger
Date :  25 Jul 14  (Deposition) - 10 Dec 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta Barrel, Transfer Protein, Kidney, Liver, Retinol-Binding Prot, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Nossoni, Z. Assar, I. Yapici, M. Nosrati, W. Wang, T. Berbasova, C. Vasileiou, B. Borhan, J. Geiger
Structures Of Holo Wild-Type Human Cellular Retinol-Binding Protein Ii (Hcrbpii) Bound To Retinol And Retinal.
Acta Crystallogr. , Sect. D V. 70 3226 2014
PubMed-ID: 25478840  |  Reference-DOI: 10.1107/S1399004714023839

(-) Compounds

Molecule 1 - RETINOL-BINDING PROTEIN 2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TRANSFER PROTEIN
    Gene: RBP2, CRBP2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELLULAR RETINOL-BINDING PROTEIN II, CRBP-II

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2RET3Ligand/IonRETINAL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2RET1Ligand/IonRETINAL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2RET1Ligand/IonRETINAL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2RET1Ligand/IonRETINAL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2RET-1Ligand/IonRETINAL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:16 , THR A:51 , PHE A:57 , SER A:76 , LEU A:77 , TRP A:106 , LEU A:119 , HOH A:358BINDING SITE FOR RESIDUE RET A 201
2AC2SOFTWAREPHE B:16 , LYS B:40 , THR B:51 , THR B:53 , LEU B:77 , TRP B:106 , GLN B:108 , HOH B:310BINDING SITE FOR RESIDUE RET B 201
3AC3SOFTWAREASP B:24 , ASP B:26 , ASP B:78 , HOH B:357BINDING SITE FOR RESIDUE ACT B 202
4AC4SOFTWARETHR A:1 , ASP A:91 , ASP B:63BINDING SITE FOR RESIDUE ACT B 203
5AC5SOFTWAREVAL B:34 , HOH B:375 , HOH C:308 , HOH C:324 , HOH C:337BINDING SITE FOR RESIDUE ACT B 204
6AC6SOFTWAREILE C:25 , LYS C:40 , THR C:51 , VAL C:62 , PHE C:64 , LEU C:77 , TRP C:106 , ACT C:202 , HOH C:304BINDING SITE FOR RESIDUE RET C 201
7AC7SOFTWARETYR C:60 , GLU C:72 , GLN C:97 , RET C:201 , HOH C:386BINDING SITE FOR RESIDUE ACT C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QYP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QYP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QYP)

(-) 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:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeee.....eeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeee...eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyp A   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeee....eeeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyp B   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeee.....eeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyp C   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain D from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhhh..hhhhhhhhhhh..eeeeeee..eeeeeee....eeeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyp D   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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  (0, 0)

(no "SCOP Domain" information available for 4QYP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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        RET2_HUMAN | P50120: 2rcq 2rct 4ede 4eej 4efg 4exz 4gkc 4qyn 4qzt 4qzu 4ruu 4zcb 4zgu 4zh6 4zh9 4zj0 4zr2 5dg4 5dpq 5f58 5f6b 5f7g 5faz 5fen 5ffh

(-) Related Entries Specified in the PDB File

4qyn