1ZY3 - JenaLib

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NMR Structure - model 1 (Jmol Viewer)

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Title :   STRUCTURAL MODEL OF COMPLEX OF BCL-W PROTEIN WITH BID BH3-PEPTIDE

Authors :   A. Y. Denisov, K. Gehring

Date :   09 Jun 05 (Deposition) - 14 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)

Keywords :   Apoptosis, Bcl-W, Bh3-Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Y. Denisov, G. Chen, T. Sprules, T. Moldoveanu, P. Beauparlant, K. Gehring
Structural Model Of The Bcl-W-Bid Peptide Complex And Its Interactions With Phospholipid Micelles.
Biochemistry V. 45 2250 2006
PubMed-ID: 16475813 | Reference-DOI: 10.1021/BI052332S
(for further references see the PDB file header)

Molecule 1 - APOPTOSIS REGULATOR BCL-W
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET-29B+
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-171
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BCL-2-LIKE 2 PROTEIN

Molecule 2 - BH3-PEPTIDE FROM BH3 INTERACTING DOMAIN DEATH AGONIST PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BID


NMR Structure (10x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ZY3)

(no "Site" information available for 1ZY3)

(no "SS Bond" information available for 1ZY3)

(no "Cis Peptide Bond" information available for 1ZY3)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048418	Q	133	R	B2CL2_HUMAN	Polymorphism	910332	A	R	132	R

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

NMR Structure (6, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BH4_1	PS01260	Apoptosis regulator, Bcl-2 family BH4 motif signature.	B2CL2_HUMAN	9-29	1	A:8-28
2	BH4_2	PS50063	Apoptosis regulator, Bcl-2 family BH4 motif profile.	B2CL2_HUMAN	10-27	1	A:9-26
3	BCL2_FAMILY	PS50062	BCL2-like apoptosis inhibitors family profile.	B2CL2_HUMAN	46-146	1	A:45-145
4	BH1	PS01080	Apoptosis regulator, Bcl-2 family BH1 motif signature.	B2CL2_HUMAN	85-104	1	A:84-103
5	BH3	PS01259	Apoptosis regulator, Bcl-2 family BH3 motif signature.	BID_HUMAN	86-100	1	B:205-219
6	BH2	PS01258	Apoptosis regulator, Bcl-2 family BH2 motif signature.	B2CL2_HUMAN	137-148	1	A:136-147

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000250405	1	ENSE00001031653	chr14:23776026-23776103	78	B2CL2_HUMAN	-	0	0	-	-
1.2	ENST00000250405	2	ENSE00001031651	chr14:23776401-23776488	88	B2CL2_HUMAN	-	0	0	-	-
1.3	ENST00000250405	3	ENSE00000889210	chr14:23776969-23777408	440	B2CL2_HUMAN	1-144	144	1	A:1-143	143
1.4	ENST00000250405	4	ENSE00001031652	chr14:23778025-23780968	2944	B2CL2_HUMAN	145-193	49	1	A:144-170	27

2.1b	ENST00000399774	1b	ENSE00001540140	chr22:18257258-18257147	112	BID_HUMAN	-	0	0	-	-
2.3	ENST00000399774	3	ENSE00002194975	chr22:18232940-18232871	70	BID_HUMAN	1-4	4	0	-	-
2.4	ENST00000399774	4	ENSE00001752867	chr22:18226779-18226569	211	BID_HUMAN	5-75	71	0	-	-
2.5d	ENST00000399774	5d	ENSE00001643928	chr22:18222254-18222115	140	BID_HUMAN	75-121	47	1	B:201-220	20
2.6b	ENST00000399774	6b	ENSE00001767385	chr22:18220995-18220783	213	BID_HUMAN	122-192	71	0	-	-
2.7e	ENST00000399774	7e	ENSE00001856820	chr22:18218357-18216937	1421	BID_HUMAN	193-195	3	0	-	-

NMR Structure

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:170
 aligned with B2CL2_HUMAN | Q92843 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
          B2CL2_HUMAN     2 ATPASAPDTRALVADFVGYKLRQKGYVCGAGPGEGPAADPLHQAMRAAGDEFETRFRRTFSDLAAQLHVTPGSAQQRFTQVSDELFQGGPNWGRLVAFFVFGAALCAESVNKEMEPLVGQVQEWMVAYLETQLADWIHSSGGWAEFTALYGDGALEEARRLREGNWASVR 171
               SCOP domains d1zy3a1 A:1-170 Apoptosis regulator Bcl-w                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----BH4-1zy3A01 A:5-31         -------------Bcl-2-1zy3A02 A:45-143                                                                             --------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------R-------------------------------------- SAPs(SNPs)
                PROSITE (1) -------BH4_1  PDB: A:8-28   ----------------BCL2_FAMILY  PDB: A:45-145 UniProt: 46-146                                                           ------------------------- PROSITE (1)
                PROSITE (2) --------BH4_2  PDB: A:9-26---------------------------------------------------------BH1  PDB: A:84-103  --------------------------------BH2         ----------------------- PROSITE (2)
               Transcript 1 Exon 1.3  PDB: A:1-143 UniProt: 1-144 [INCOMPLETE]                                                                                             Exon 1.4  PDB: A:144-170    Transcript 1
                 1zy3 A   1 ATPASAPDTRALVADFVGYKLRQKGYVCGAGPGEGPAADPLHQAMRAAGDEFETRFRRTFSDLAAQLHVTPGSAQQRFTQVSDELFQGGPNWGRLVAFFVFGAALCAESVNKEMEVLVGQVQEWMVAYLETRLADWIHSSGGWAEFTALYGDGALEEARRLREGNWASVR 170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:20
 aligned with BID_HUMAN | P55957 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:20
                                    91       101
            BID_HUMAN    82 IIRNIARHLAQVGDSMDRSI 101
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains BID-1zy3B01          Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                PROSITE (2) -------------------- PROSITE (2)
                PROSITE (3) ----BH3            - PROSITE (3)
               Transcript 2 Exon 2.5d            Transcript 2
                 1zy3 B 201 IIKNIARHLAQVGDSMDRSI 220
                                   210       220

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 "CATH Domain" information available for 1ZY3)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: BH4] (30)

Family: BH4 (30)

Homo sapiens (Human) (26)

BH4-1zy3A01

A:5-31

Clan: no clan defined [family: BID] (3)

Family: BID (3)

Homo sapiens (Human) (2)

BID-1zy3B01

B:201-220

Clan: no clan defined [family: Bcl-2] (60)

Family: Bcl-2 (60)

Homo sapiens (Human) (44)

Bcl-2-1zy3A02

A:45-143

NMR Structure(hide GO term definitions)

Chain A (B2CL2_HUMAN | Q92843)

molecular function
	GO:0051400	BH domain binding	Interacting selectively and non-covalently with the Bcl-2 homology (BH) domain of a protein. Bcl-2-related proteins share homology in one to four conserved regions designated the Bcl-2 homology (BH) domains BH1, BH2, BH3 and BH4. These domains contribute at multiple levels to the function of these proteins in cell death and survival. Anti-apoptotic members of the Bcl-2 family have four BH domains (BH1-BH4). Pro-apoptotic members have fewer BH domains.
	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).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0060011	Sertoli cell proliferation	The multiplication or reproduction of Sertoli cells, resulting in the expansion of the Sertoli cell population. A Sertoli cell is a supporting cell projecting inward from the basement membrane of seminiferous tubules.
	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:0097192	extrinsic apoptotic signaling pathway in absence of ligand	A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
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.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031966	mitochondrial membrane	Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	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.

Chain B (BID_HUMAN | P55957)

molecular function
	GO:0005123	death receptor binding	Interacting selectively and non-covalently with any member of the death receptor (DR) family. The DR family falls within the tumor necrosis factor receptor superfamily and is characterized by a cytoplasmic region of ~80 residues termed the death domain (DD).
	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).
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
	GO:0008637	apoptotic mitochondrial changes	The morphological and physiological alterations undergone by mitochondria during apoptosis.
	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:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0090150	establishment of protein localization to membrane	The directed movement of a protein to a specific location in a membrane.
	GO:0097191	extrinsic apoptotic signaling pathway	A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.
	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered.
	GO:0034349	glial cell apoptotic process	Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system.
	GO:0097284	hepatocyte apoptotic process	Any apoptotic process in a hepatocyte, the main structural component of the liver.
	GO:0097345	mitochondrial outer membrane permeabilization	The process by which the mitochondrial outer membrane becomes permeable to the passing of proteins and other molecules from the intermembrane space to the cytosol as part of the apoptotic signaling pathway.
	GO:0051402	neuron apoptotic process	Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:2001238	positive regulation of extrinsic apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
	GO:2001244	positive regulation of intrinsic apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:1901030	positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway.
	GO:0032464	positive regulation of protein homooligomerization	Any process that activates or increases the frequency, rate or extent of protein homooligomerization.
	GO:1900740	positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
	GO:0032461	positive regulation of protein oligomerization	Any process that activates or increases the frequency, rate or extent of protein oligomerization.
	GO:0090200	positive regulation of release of cytochrome c from mitochondria	Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0006626	protein targeting to mitochondrion	The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
	GO:2000045	regulation of G1/S transition of mitotic cell cycle	Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:1902108	regulation of mitochondrial membrane permeability involved in apoptotic process	Any regulation of mitochondrial membrane permeability that is involved in apoptotic process.
	GO:0032459	regulation of protein oligomerization	Any process that modulates the frequency, rate or extent of protein oligomerization.
	GO:0001836	release of cytochrome c from mitochondria	The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation.
	GO:0032355	response to estradiol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0042770	signal transduction in response to DNA damage	A cascade of processes induced by the detection of DNA damage within a cell.
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.
	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:0032592	integral component of mitochondrial membrane	The component of the mitochondrial membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031966	mitochondrial membrane	Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	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.

NMR Structure
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	1zy3
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	BID_HUMAN \| P55957
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Description

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Ligands, Modified Residues, Ions (0, 0)

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Sequence-Structure Mapping

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