2RCQ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN APO CELLULAR RETINOL BINDING PROTEIN II (CRBP-II)

Authors :   H. L. Monaco, S. Capaldi, M. Perduca

Date :   20 Sep 07 (Deposition) - 02 Oct 07 (Release) - 14 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A

Keywords :   Cellular Retinol Binding Protein Ii, Crbp-Ii, Retinol, Lipid-Binding Protein, Retinol-Binding, Transport, Vitamin A, Retinol-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Tarter, S. Capaldi, M. E. Carrizo, E. Ambrosi, M. Perduca, H. L. Monaco
Crystal Structure Of Human Cellular Retinol-Binding Protein Ii To 1. 2 A Resolution.
Proteins V. 70 1626 2007
PubMed-ID: 18076076 | Reference-DOI: 10.1002/PROT.21848

Molecule 1 - RETINOL-BINDING PROTEIN II, CELLULAR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE50
	Expression System Strain	:	SG13009
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RBP2, CRBP2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CRBP-II

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:26 , PHE A:27 , ARG A:30 , HOH A:206 , HOH A:242 , HOH A:260 , HOH A:274 , HOH A:297	BINDING SITE FOR RESIDUE SO4 A 151
2	AC2	SOFTWARE	ARG A:58 , LYS A:98 , HOH A:202 , HOH A:226 , HOH A:285	BINDING SITE FOR RESIDUE SO4 A 152
3	AC3	SOFTWARE	ASN A:13 , GLU A:14 , ASN A:15 , PHE A:16 , GLU A:17 , ARG A:35 , LYS A:133 , HOH A:167 , HOH A:207 , HOH A:229 , HOH A:249	BINDING SITE FOR RESIDUE TLA A 150

(no "SS Bond" information available for 2RCQ)

(no "Cis Peptide Bond" information available for 2RCQ)

(no "SAP(SNP)/Variant" information available for 2RCQ)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FABP	PS00214	Cytosolic fatty-acid binding proteins signature.	RET2_HUMAN	7-24	1	A:6-23

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000232217	3a	ENSE00002067741	chr3:139195358-139195229	130	RET2_HUMAN	1-25	25	1	A:0-24	25
1.4	ENST00000232217	4	ENSE00000778977	chr3:139181132-139180954	179	RET2_HUMAN	25-84	60	1	A:24-83	60
1.5b	ENST00000232217	5b	ENSE00000778975	chr3:139173672-139173571	102	RET2_HUMAN	85-118	34	1	A:84-117	34
1.6	ENST00000232217	6	ENSE00000794927	chr3:139172008-139171726	283	RET2_HUMAN	119-134	16	1	A:118-133	16

Asymmetric/Biological 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:141
 aligned with RET2_HUMAN | P50120 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:141
                               1                                                                                                                                  134    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127      |  - 
           RET2_HUMAN     - ---MTRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKK----   -
               SCOP domains d2rcqa_ A: automated matches                                                                                                                  SCOP domains
               CATH domains 2rcqA00 A:-3-137  [code=2.40.128.20, no name defined]                                                                                         CATH domains
               Pfam domains --------Lipocalin-2rcqA01 A:5-133                                                                                                        ---- Pfam domains
         Sec.struct. author .........eeeeeeeeehhhhhhhhh..hhhhhhhhh....eeeeeee..eeeeeee.......eeee....eeee.......eeeeeeeee..eeeeeee......eeeeeee..eeeeeeee..eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FABP  PDB: A:6-23 ------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) ---Exon 1.3a  PDB: A:0-24   -----------------------------------------------------------Exon 1.5b  PDB: A:84-117          Exon 1.6        ---- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.4  PDB: A:24-83 UniProt: 25-84                       ------------------------------------------------------ Transcript 1 (2)
                 2rcq A  -3 MRGSTRDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKVIDQDGDNFKTKTTSTFRNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKQWIEGDKLYLELTCGDQVCRQVFKKKLVPR 137
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Fatty acid binding protein-like (183)

Protein domain: automated matches (26)

Human (Homo sapiens) [TaxId: 9606] (15)

d2rcqa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.20, no name defined] (352)

Human (Homo sapiens) (91)

2rcqA00

A:-3-137

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Calycin (163)

Family: Lipocalin (123)

Homo sapiens (Human) (41)

Lipocalin-2rcqA01

A:5-133

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RET2_HUMAN | P50120)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0016918	retinal binding	Interacting selectively and non-covalently with retinal, one of the forms of vitamin A. Retinal plays an important role in the visual process in most vertebrates, combining with opsins to form visual pigments in the retina.
	GO:0005501	retinoid binding	Interacting selectively and non-covalently with retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
	GO:0019841	retinol binding	Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0008544	epidermis development	The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
	GO:0001523	retinoid metabolic process	The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0006776	vitamin A metabolic process	The chemical reactions and pathways involving any of the vitamin A compounds, retinol, retinal (retinaldehyde) and retinoic acid, all of which are derivatives of beta-carotene.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TLA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rcq)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2rcq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RET2_HUMAN \| P50120
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RET2_HUMAN \| P50120
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File