3R8J - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN SOUL PROTEIN (ORTHORHOMBIC FORM)

Authors :   E. K. Ambrosi, S. Capaldi, M. Bovi, G. Saccomani, M. Perduca, H. L. Monac

Date :   24 Mar 11 (Deposition) - 29 Jun 11 (Release) - 24 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Hebp Family, Soul Protein, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ambrosi, S. Capaldi, M. Bovi, G. Saccomani, M. Perduca, H. L. Monaco
Structural Changes In The Bh3 Domain Of Soul Protein Upon Interaction With The Anti-Apoptotic Protein Bcl-Xl.
Biochem. J. V. 438 291 2011
PubMed-ID: 21639858 | Reference-DOI: 10.1042/BJ20110257

Molecule 1 - HEME-BINDING PROTEIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE50
	Expression System Strain	:	BL21 C41
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	C6ORF34, HEBP2, SOUL
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PLACENTAL PROTEIN 23, PP23, PROTEIN SOUL

		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, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:184 , ARG A:188 , HOH A:243 , HOH A:330 , HOH A:365 , PRO B:35 , GLY B:36 , SER B:37 , TYR B:38 , ASP B:165	BINDING SITE FOR RESIDUE PO4 A 500

(no "SS Bond" information available for 3R8J)

Asymmetric Unit

No.	Residues
1	Asp A:30	-	Ala A:31
2	Ala A:87	-	Pro A:88
3	Ser A:181	-	Pro A:182
4	Glu B:29	-	Asp B:30
5	Ala B:87	-	Pro B:88
6	Ser B:181	-	Pro B:182

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053364	R	140	Q	HEBP2_HUMAN	Polymorphism	3734303	A/B	R	140	Q
2	UniProt	VAR_053365	E	191	A	HEBP2_HUMAN	Polymorphism	14812	A/B	E	191	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053364	R	140	Q	HEBP2_HUMAN	Polymorphism	3734303	A	R	140	Q
2	UniProt	VAR_053365	E	191	A	HEBP2_HUMAN	Polymorphism	14812	A	E	191	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053364	R	140	Q	HEBP2_HUMAN	Polymorphism	3734303	B	R	140	Q
2	UniProt	VAR_053365	E	191	A	HEBP2_HUMAN	Polymorphism	14812	B	E	191	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3R8J)

(no "Exon" information available for 3R8J)

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:180
 aligned with HEBP2_HUMAN | Q9Y5Z4 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:180
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198
          HEBP2_HUMAN    19 AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN 198
               SCOP domains d3r8ja_ A: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee............eeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhh..............eeeeee........eeeeeeee.hhhhhh.........eeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhh........eeeee...........eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------A------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r8j A  19 AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN 198
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with HEBP2_HUMAN | Q9Y5Z4 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:180
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198
          HEBP2_HUMAN    19 AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN 198
               SCOP domains d3r8jb_ B: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) SOUL-3r8jB01 B:19-197                                                                                                                                                              - Pfam domains (1)
           Pfam domains (2) SOUL-3r8jB02 B:19-197                                                                                                                                                              - Pfam domains (2)
         Sec.struct. author ......ee............eeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhh..............eeeeee.........eeeeeee.hhhhhh.........eeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhh........eeeee...........eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------A------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r8j B  19 AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN 198
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Probable bacterial effector-binding domain (17)

Superfamily: Probable bacterial effector-binding domain (17)

Family: automated matches (2)

Protein domain: automated matches (2)

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

1a	d3r8ja_	A:
1b	d3r8jb_	B:

(no "CATH Domain" information available for 3R8J)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SHS2 (26)

Family: SOUL (3)

Homo sapiens (Human) (3)

1a	SOUL-3r8jB01	B:19-197
1b	SOUL-3r8jB02	B:19-197

Asymmetric Unit(hide GO term definitions)

Chain A,B (HEBP2_HUMAN | Q9Y5Z4)

molecular function
	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:0010917	negative regulation of mitochondrial membrane potential	Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or extent of a mitochondrial membrane potential, the electric potential existing across any mitochondrial membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
	GO:0035794	positive regulation of mitochondrial membrane permeability	Any process that increases the frequency, rate or extent of the passage or uptake of molecules by the mitochondrial membrane.
	GO:0010940	positive regulation of necrotic cell death	Any process that increases the rate, frequency or extent of necrotic cell death. Necrotic cell death is a cell death process that is morphologically characterized by a gain in cell volume (oncosis), swelling of organelles, plasma membrane rupture and subsequent loss of intracellular contents.
	GO:1901031	regulation of response to reactive oxygen species	Any process that modulates the frequency, rate or extent of response to reactive oxygen species.
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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:87 - Pro A:88	[ RasMol ]
		Ala B:87 - Pro B:88	[ RasMol ]
		Asp A:30 - Ala A:31	[ RasMol ]
		Glu B:29 - Asp B:30	[ RasMol ]
		Ser A:181 - Pro A:182	[ RasMol ]
		Ser B:181 - Pro B:182	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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UniProtKB/Swiss-Prot
	HEBP2_HUMAN \| Q9Y5Z4	:	3r85 3r8k 4ayz 4b0y 5gqq

3r85	BH3 DOMAIN CONTAINING PEPTIDE OF SOUL PROTEIN IN COMPLEX WITH BCL-XL
3r8k	HUMAN SOUL PROTEIN (HEXAGONAL FORM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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