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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD TYPE HUMAN CELLULAR RETINOL BINDING PROTEIN II (HCRBPII) BOUND TO RETINOL AT 11 KEV BEAM ENERGY
 
Authors :  Z. Assar, J. H. Geiger
Date :  28 Jul 14  (Deposition) - 10 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Retinol, Human Cellular Retinol Binding Protein Ii, Intracellular Lipid Binding Protein, X-Ray Flux, X-Ray Damage, Retinal, Retinoid Chaperones, Protein Binding (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, C, B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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):   C 
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3RTL3Ligand/IonRETINOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3RTL1Ligand/IonRETINOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3RTL1Ligand/IonRETINOL
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3RTL1Ligand/IonRETINOL
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3RTL-1Ligand/IonRETINOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:16 , ILE A:25 , GLN A:38 , LYS A:40 , THR A:51 , ARG A:58 , LEU A:77 , TRP A:106 , GLN A:108 , GOL A:203 , HOH A:351BINDING SITE FOR RESIDUE RTL A 201
02AC2SOFTWAREVAL A:34 , HOH A:355 , ASN C:13BINDING SITE FOR RESIDUE ACT A 202
03AC3SOFTWARETYR A:19 , TYR A:60 , GLU A:72 , LEU A:77 , GLN A:97 , ARG A:104 , TRP A:106 , RTL A:201 , HOH A:314BINDING SITE FOR RESIDUE GOL A 203
04AC4SOFTWAREPHE C:16 , GLN C:38 , LYS C:40 , LEU C:77 , TRP C:106 , GLN C:108 , ACT C:202 , HOH C:373BINDING SITE FOR RESIDUE RTL C 201
05AC5SOFTWAREGLU C:72 , GLN C:97 , TRP C:106 , RTL C:201 , HOH C:314BINDING SITE FOR RESIDUE ACT C 202
06AC6SOFTWAREPHE B:16 , GLN B:38 , LYS B:40 , TYR B:60 , LEU B:77 , TRP B:106 , GLN B:108 , ACT B:202 , HOH B:359BINDING SITE FOR RESIDUE RTL B 201
07AC7SOFTWARETYR B:19 , TYR B:60 , GLN B:97 , ARG B:104 , TRP B:106 , RTL B:201 , HOH B:302BINDING SITE FOR RESIDUE ACT B 202
08AC8SOFTWARETYR B:116 , VAL B:129 , HOH B:344 , PHE C:57 , ARG C:58BINDING SITE FOR RESIDUE ACT B 203
09AC9SOFTWAREASP B:71 , LYS B:83 , ASP D:71 , HIS D:81 , VAL D:82BINDING SITE FOR RESIDUE ACT D 201
10BC1SOFTWAREASP A:61 , LYS A:75 , TRP D:109 , GLU D:111 , HOH D:329 , HOH D:332 , HOH D:358BINDING SITE FOR RESIDUE ACT D 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QZU)

(-) 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......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qzu 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..hhhhhhhhhh...eeeeeee..eeeeeee.....eeeeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qzu 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
                 4qzu 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..hhhhhhh......eeeeeee..eeeeeee.......eeee....ee...........eeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qzu D   1 TRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4QZU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

2rcq 2rct 4ede 4eej 4efg 4qzt