2QS9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE HUMAN RETINOBLASTOMA-BINDING PROTEIN 9 (RBBP-9). NESG TARGET HR2978

Authors :   S. M. Vorobiev, M. Su, J. Seetharaman, A. Kuzin, C. X. Chen, K. Cunningham, L. Owens, M. Maglaqui, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   30 Jul 07 (Deposition) - 14 Aug 07 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Retinoblastoma-Binding Protein 9, Retinoblastoma-Binding Protein 10, B5T Overexpressed Gene Protein, Bog, Rbbp9, Rbbp10, Hr2978, Nesg, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Alternative Splicing, Cytoplasm, Nucleus, Phosphorylation, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Vorobiev, M. Su, J. Seetharaman, Y. J. Huang, C. X. Chen, M. Maglaqui, H. Janjua, M. Proudfoot, A. Yakunin, R. Xiao, T. B. Acton, G. T. Montelione, L. Tong
Crystal Structure Of Human Retinoblastoma Binding Protein 9.
Proteins V. 74 526 2008
PubMed-ID: 19004028 | Reference-DOI: 10.1002/PROT.22278
(for further references see the PDB file header)

Molecule 1 - RETINOBLASTOMA-BINDING PROTEIN 9
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21-23C
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RBBP9, BOG, RBBP10
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RBBP-9, RETINOBLASTOMA-BINDING PROTEIN 10, RBBP- 10, B5T OVEREXPRESSED GENE PROTEIN, BOG PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2QS9)

(no "SS Bond" information available for 2QS9)

(no "Cis Peptide Bond" information available for 2QS9)

(no "SAP(SNP)/Variant" information available for 2QS9)

(no "PROSITE Motif" information available for 2QS9)

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000337227	1a	ENSE00001252529	chr20:18477887-18477713	175	RBBP9_HUMAN	1-33	33	2	A:3-33 B:3-33	31 31
1.2	ENST00000337227	2	ENSE00000859319	chr20:18476524-18476482	43	RBBP9_HUMAN	34-48	15	2	A:34-48 B:34-48	15 15
1.3	ENST00000337227	3	ENSE00000859318	chr20:18474707-18474602	106	RBBP9_HUMAN	48-83	36	2	A:48-83 B:48-83	36 36
1.4	ENST00000337227	4	ENSE00000859316	chr20:18471124-18471039	86	RBBP9_HUMAN	83-112	30	2	A:83-112 B:83-112	30 30
1.5d	ENST00000337227	5d	ENSE00001342801	chr20:18470634-18467184	3451	RBBP9_HUMAN	112-186	75	2	A:112-186 B:112-182	75 71

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:192
 aligned with RBBP9_HUMAN | O75884 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:192
                                                                                                                                                                                                                 186        
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   |     -  
          RBBP9_HUMAN     3 SPSKAVIVPGNGGGDVTTHGWYGWVKKELEKIPGFQCLAKNMPDPITARESIWLPFMETELHCDEKTIIIGHSSGAIAAMRYAETHRVYAIVLVSAYTSDLGDENERASGYFTRPWQWEKIKANCPYIVQFGSTDDPFLPWKEQQEVADRLETKLHKFTDCGHFQNTEFHELITVVKSLLKVPA--------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2qs9A00 A:3-194  [code=3.40.50.1820, no name defined]                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee............hhhhhhhhhh......eee.........hhhhhhhhhhhh......eeeeeehhhhhhhhhhhhhh...eeeee........hhhhhhh.......hhhhhhhhh.eeeeeee......hhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:3-33         Exon 1.2       ----------------------------------Exon 1.4  PDB: A:83-112       ---------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:48-83              ----------------------------Exon 1.5d  PDB: A:112-186 UniProt: 112-186                                 -------- Transcript 1 (2)
                 2qs9 A   3 SPSKAVIVPGNGGGDVTTHGWYGWVKKELEKIPGFQCLAKNmPDPITARESIWLPFmETELHCDEKTIIIGHSSGAIAAmRYAETHRVYAIVLVSAYTSDLGDENERASGYFTRPWQWEKIKANCPYIVQFGSTDDPFLPWKEQQEVADRLETKLHKFTDCGHFQNTEFHELITVVKSLLKVPALEHHHHHH 194
                                    12        22        32        42 |      52      | 62        72        82        92       102       112       122       132       142       152       162       172       182       192  
                                                                    44-MSE         59-MSE                 82-MSE

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with RBBP9_HUMAN | O75884 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:180
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
          RBBP9_HUMAN     3 SPSKAVIVPGNGGGDVTTHGWYGWVKKELEKIPGFQCLAKNMPDPITARESIWLPFMETELHCDEKTIIIGHSSGAIAAMRYAETHRVYAIVLVSAYTSDLGDENERASGYFTRPWQWEKIKANCPYIVQFGSTDDPFLPWKEQQEVADRLETKLHKFTDCGHFQNTEFHELITVVKSLL 182
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2qs9B00 B:3-182  [code=3.40.50.1820, no name defined]                                                                                                                                CATH domains
           Pfam domains (1) ----Ser_hydrolase-2qs9B01 B:7-182                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ----Ser_hydrolase-2qs9B02 B:7-182                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ...eeeee............hhhhhhhhhh.....eee..........hhhhhhhhhhhh......eeeeeehhhhhhhhhhh......eeeee........hhhhhhh.......hhhhhhhhh.eeeeeee......hhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:3-33         Exon 1.2       ----------------------------------Exon 1.4  PDB: B:83-112       ---------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: B:48-83              ----------------------------Exon 1.5d  PDB: B:112-182 UniProt: 112-186 [INCOMPLETE]                 Transcript 1 (2)
                 2qs9 B   3 SPSKAVIVPGNGGGDVTTHGWYGWVKKELEKIPGFQCLAKNmPDPITARESIWLPFmETELHCDEKTIIIGHSSGAIAAmRYAETHRVYAIVLVSAYTSDLGDENERASGYFTRPWQWEKIKANCPYIVQFGSTDDPFLPWKEQQEVADRLETKLHKFTDCGHFQNTEFHELITVVKSLL 182
                                    12        22        32        42 |      52      | 62        72        82        92       102       112       122       132       142       152       162       172       182
                                                                    44-MSE         59-MSE                 82-MSE

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 '\|'

(no "SCOP Domain" information available for 2QS9)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Human (Homo sapiens) (118)

1a	2qs9A00	A:3-194
1b	2qs9B00	B:3-182

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AB_hydrolase (347)

Family: Ser_hydrolase (2)

Homo sapiens (Human) (1)

1a	Ser_hydrolase-2qs9B01	B:7-182
1b	Ser_hydrolase-2qs9B02	B:7-182

Asymmetric Unit(hide GO term definitions)

Chain A,B (RBBP9_HUMAN | O75884)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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Description

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Ligands, Modified Residues, Ions (1, 6)

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