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Description

Title :   CRYSTAL STRUCTURE OF THE SCAN DOMAIN FROM HUMAN PATERNALLY EXPRESSED GENE 3 PROTEIN

Authors :   V. Rimsa, T. C. Eadsforth, W. N. Hunter

Date :   09 Apr 13 (Deposition) - 17 Apr 13 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Dna Binding Protein, Peg3 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Rimsa, T. C. Eadsforth, W. N. Hunter
Structure Of The Scan Domain Of Human Paternally Expressed Gene 3 Protein.
Plos One V. 8 69538 2013
PubMed-ID: 23936039 | Reference-DOI: 10.1371/JOURNAL.PONE.0069538

Compounds

Molecule 1 - PATERNALLY-EXPRESSED GENE 3 PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD
	Expression System Vector	:	PET15B
	Expression System Vector Type	:	PLASMID
	Fragment	:	SCAN DOMAIN, RESIDUES 40-130
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ZINC FINGER AND SCAN DOMAIN-CONTAINING PROTEIN 24

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 27)

Asymmetric Unit (3, 27)

No.	Name	Count	Type	Full Name
1	EDO	21	Ligand/Ion	1,2-ETHANEDIOL
2	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
2	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
2	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Sites (27, 27)

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:56 , THR A:59 , HOH A:2065 , HOH A:2066 , ARG B:13 , GLU B:55	BINDING SITE FOR RESIDUE PEG A 1091
02	AC2	SOFTWARE	HIS A:9 , TRP A:37 , LEU A:51 , LEU A:58 , EDO A:1104 , EDO A:1105 , HOH A:2044	BINDING SITE FOR RESIDUE PEG A 1092
03	AC3	SOFTWARE	HIS B:1 , THR B:42 , ARG B:43 , HOH B:2034 , HOH B:2036	BINDING SITE FOR RESIDUE PEG B 1093
04	AC4	SOFTWARE	TYR A:17 , GLU A:19 , GLY A:22 , PRO A:23 , HOH A:2020 , LYS B:88	BINDING SITE FOR RESIDUE PEG A 1093
05	AC5	SOFTWARE	EDO A:1100 , HIS B:9 , TRP B:37 , GLU B:55 , LEU B:58 , THR B:59 , HOH B:2009 , HOH B:2071	BINDING SITE FOR RESIDUE PGE B 1094
06	AC6	SOFTWARE	GLN A:39 , THR A:42 , ARG A:43 , HOH A:2005 , HOH A:2040 , HOH A:2068 , ARG B:70	BINDING SITE FOR RESIDUE PGE A 1094
07	AC7	SOFTWARE	LEU A:58 , LYS A:66 , HOH A:2048 , HOH A:2069	BINDING SITE FOR RESIDUE EDO A 1095
08	AC8	SOFTWARE	LYS A:45 , ARG B:43 , THR B:44 , EDO B:1097 , HOH B:2037 , HOH B:2073	BINDING SITE FOR RESIDUE EDO B 1095
09	AC9	SOFTWARE	THR A:59 , GLU A:63 , LYS A:66 , HOH A:2047 , HOH A:2050 , THR B:44 , GLU B:46 , GLU B:47 , HOH B:2074	BINDING SITE FOR RESIDUE EDO B 1096
10	BC1	SOFTWARE	ASP A:4 , PHE A:7 , EDO A:1099 , PRO B:67 , ALA B:71	BINDING SITE FOR RESIDUE EDO A 1096
11	BC2	SOFTWARE	ARG A:13 , ASN A:14 , LYS A:45 , GLU B:41 , EDO B:1095	BINDING SITE FOR RESIDUE EDO B 1097
12	BC3	SOFTWARE	ASN A:32 , ASP A:36 , HOH A:2031 , ASN B:86 , TYR B:87	BINDING SITE FOR RESIDUE EDO B 1098
13	BC4	SOFTWARE	ASN B:14 , LEU B:15 , ILE B:16 , HOH B:2075 , HOH B:2076	BINDING SITE FOR RESIDUE EDO B 1099
14	BC5	SOFTWARE	ARG A:24 , THR B:82 , GLU B:85 , HOH B:2077	BINDING SITE FOR RESIDUE EDO B 1100
15	BC6	SOFTWARE	ILE A:16 , LEU B:35 , EDO B:1104 , HOH B:2078 , HOH B:2079 , HOH B:2080	BINDING SITE FOR RESIDUE EDO B 1101
16	BC7	SOFTWARE	PHE A:20 , LYS A:25 , GLU B:89	BINDING SITE FOR RESIDUE EDO A 1097
17	BC8	SOFTWARE	PRO A:67 , ARG A:70 , HOH A:2056 , ASP B:4	BINDING SITE FOR RESIDUE EDO A 1098
18	BC9	SOFTWARE	ASP A:4 , GLN A:10 , EDO A:1096	BINDING SITE FOR RESIDUE EDO A 1099
19	CC1	SOFTWARE	GLU A:41 , ARG A:43 , HOH A:2070 , ASN B:14 , LYS B:45 , PGE B:1094	BINDING SITE FOR RESIDUE EDO A 1100
20	CC2	SOFTWARE	ASN A:14 , ILE A:16 , VAL A:18 , TYR B:91 , GLN B:92 , HOH B:2069	BINDING SITE FOR RESIDUE EDO A 1101
21	CC3	SOFTWARE	ILE A:28 , ASN A:32 , ASN B:86	BINDING SITE FOR RESIDUE EDO B 1102
22	CC4	SOFTWARE	GLU A:63 , ASN B:76	BINDING SITE FOR RESIDUE EDO B 1103
23	CC5	SOFTWARE	ILE A:49 , GLU A:50 , HOH A:2036 , ARG B:31 , LEU B:35 , EDO B:1101	BINDING SITE FOR RESIDUE EDO B 1104
24	CC6	SOFTWARE	ASN A:32	BINDING SITE FOR RESIDUE EDO A 1102
25	CC7	SOFTWARE	MET A:2 , LYS B:73	BINDING SITE FOR RESIDUE EDO A 1103
26	CC8	SOFTWARE	SER A:5 , TRP A:37 , ARG A:43 , LEU A:51 , PEG A:1092 , EDO A:1105	BINDING SITE FOR RESIDUE EDO A 1104
27	CC9	SOFTWARE	LEU A:54 , GLU A:75 , PEG A:1092 , EDO A:1104	BINDING SITE FOR RESIDUE EDO A 1105

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SCAN_BOX	PS50804	SCAN box profile.	PEG3_HUMAN	46-125	2	A:9-88 B:9-88

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SCAN_BOX	PS50804	SCAN box profile.	PEG3_HUMAN	46-125	1	A:9-88 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SCAN_BOX	PS50804	SCAN box profile.	PEG3_HUMAN	46-125	1	- B:9-88

Exons (0, 0)

(no "Exon" information available for 4BHX)

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
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Chain A from PDB  Type:PROTEIN  Length:90
 aligned with PEG3_HUMAN | Q9GZU2 from UniProtKB/Swiss-Prot  Length:1588

    Alignment length:122
                                    15        25        35        45        55        65        75        85        95       105       115       125  
           PEG3_HUMAN     6 HLSATKPKKSWAPNLYELDSDLTKEPDVIIGEGPTDSEFFHQRFRNLIYVEFVGPRKTLIKLRNLCLDWLQPETRTKEEIIELLVLEQYLTIIPEKLKPWVRAKKPENCEKLVTLLENYKEM 127
               SCOP domains d4                                bhxa_ A: automated matches                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------------------------------.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------SCAN_BOX  PDB: A:9-88 UniProt: 46-125                                           -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhx A   1 HM--------------------------------TDSEFFHQRFRNLIYVEFVGPRKTLIKLRNLCLDWLQPETRTKEEIIELLVLEQYLTIIPEKLKPWVRAKKPENCEKLVTLLENYKEM  90
                             |       -         -         -    |    8        18        28        38        48        58        68        78        88  
                             2                                3

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with PEG3_HUMAN | Q9GZU2 from UniProtKB/Swiss-Prot  Length:1588

    Alignment length:124
                                    15        25        35        45        55        65        75        85        95       105       115       125    
           PEG3_HUMAN     6 HLSATKPKKSWAPNLYELDSDLTKEPDVIIGEGPTDSEFFHQRFRNLIYVEFVGPRKTLIKLRNLCLDWLQPETRTKEEIIELLVLEQYLTIIPEKLKPWVRAKKPENCEKLVTLLENYKEMYQ 129
               SCOP domains d4                                bhxb_ B: automated matches                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------------------------------.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------SCAN_BOX  PDB: B:9-88 UniProt: 46-125                                           ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhx B   1 HM--------------------------------TDSEFFHQRFRNLIYVEFVGPRKTLIKLRNLCLDWLQPETRTKEEIIELLVLEQYLTIIPEKLKPWVRAKKPENCEKLVTLLENYKEMYQ  92
                             |       -         -         -    |    8        18        28        38        48        58        68        78        88    
                             2                                3

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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 (1, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Acyl carrier protein-like (148)

Superfamily: Retrovirus capsid dimerization domain-like (45)

Family: automated matches (12)

Protein domain: automated matches (12)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d4bhxa_	A:
1b	d4bhxb_	B:

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PEG3_HUMAN | Q9GZU2)

molecular function
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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