3MQP - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN BFL-1 IN COMPLEX WITH NOXA BH3 PEPTIDE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR2930

Authors :   R. Guan, R. Xiao, L. Zhao, T. B. Acton, C. Gelinas, G. T. Montelione, Nort Structural Genomics Consortium (Nesg)

Date :   28 Apr 10 (Deposition) - 02 Jun 10 (Release) - 02 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.24

Chains :   Asym./Biol. Unit : A,B

Keywords :   Bcl-2 Family, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Guan, R. Xiao, L. Zhao, T. B. Acton, C. Gelinas, G. T. Montelione
Crystal Structure Of Human Bfl-1 In Complex With Noxa Bh3 Peptide
To Be Published
PubMed: search

Molecule 1 - BCL-2-RELATED PROTEIN A1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15
	Expression System Strain	:	BL21(DE3)+ MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BCL2A1, BCL2L5, BFL1, GRS, HBPA1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BCL-2-LIKE PROTEIN 5, BCL2-L-5, PROTEIN BFL-1, HEMOPOIETIC- SPECIFIC EARLY RESPONSE PROTEIN, PROTEIN GRS

Molecule 2 - PHORBOL-12-MYRISTATE-13-ACETATE-INDUCED PROTEIN 1
	Chains	:	B
	Engineered	:	YES
	Fragment	:	NOXA BH3 PEPTIDE, RESIDUES 19-43
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS. PEPTIDE WAS SYNTHESIZED FROM A COMMERCIAL PEPTIDE SYNTHESIS SERVICE.
	Synonym	:	PMA-INDUCED PROTEIN 1, IMMEDIATE-EARLY-RESPONSE PROTEIN APR, PROTEIN NOXA
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3MQP)

(no "Site" information available for 3MQP)

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

(no "Cis Peptide Bond" information available for 3MQP)

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020342	C	19	Y	B2LA1_HUMAN	Polymorphism	1138357	A	C	19	Y
2	UniProt	VAR_020343	N	39	K	B2LA1_HUMAN	Polymorphism	1138358	A	N	39	K
3	UniProt	VAR_020344	G	82	D	B2LA1_HUMAN	Polymorphism	3826007	A	G	82	D
4	UniProt	VAR_044059	E	117	D	B2LA1_HUMAN	Polymorphism	34080999	A	E	117	D

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BCL2_FAMILY	PS50062	BCL2-like apoptosis inhibitors family profile.	B2LA1_HUMAN	37-142	1	A:37-142
2	BH1	PS01080	Apoptosis regulator, Bcl-2 family BH1 motif signature.	B2LA1_HUMAN	78-97	1	A:78-97
3	BH2	PS01258	Apoptosis regulator, Bcl-2 family BH2 motif signature.	B2LA1_HUMAN	133-144	1	A:133-144

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000267953	1a	ENSE00001104195	chr15:80263788-80263042	747	B2LA1_HUMAN	1-140	140	1	A:2-140	139
1.3b	ENST00000267953	3b	ENSE00001832143	chr15:80253516-80253231	286	B2LA1_HUMAN	141-175	35	1	A:141-151	11

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:150
 aligned with B2LA1_HUMAN | Q16548 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
          B2LA1_HUMAN     2 TDCEFGYIYRLAQDYLQCVLQIPQPGSGPSKTSRVLQNVAFSVQKEVEKNLKSCLDNVNVVSVDTARTLFNQVMEKEFEDGIINWGRIVTIFAFEGILIKKLLRQQIAPDVDTYKEISYFVAEFIMNNTGEWIRQNGGWENGFVKKFEPK 151
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------Bcl-2-3mqpA01 A:37-140                                                                                  ----------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------Y-------------------K------------------------------------------D----------------------------------D---------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------BCL2_FAMILY  PDB: A:37-142 UniProt: 37-142                                                                --------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------BH1  PDB: A:78-97   -----------------------------------BH2         ------- PROSITE (2)
               Transcript 1 Exon 1.1a  PDB: A:2-140 UniProt: 1-140 [INCOMPLETE]                                                                                        Exon 1.3b   Transcript 1
                 3mqp A   2 TDCEFGYIYRLAQDYLQCVLQIPQPGSGPSKTSRVLQNVAFSVQKEVEKNLKSCLDNVNVVSVDTARTLFNQVMEKEFEDGIINWGRIVTIFAFEGILIKKLLRQQIAPDVDTYKEISYFVAEFIMNNTGEWIRQNGGWENGFVKKFEPK 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:25
 aligned with APR_HUMAN | Q13794 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:25
                                    28        38     
            APR_HUMAN    19 AELEVECATQLRRFGDKLNFRQKLL  43
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 3mqp B  19 AELEVECATQLRRFGDKLNFRQKLL  43
                                    28        38

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 3MQP)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Bcl-2 (60)

Homo sapiens (Human) (44)

Bcl-2-3mqpA01

A:37-140

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (B2LA1_HUMAN | Q16548)

molecular function
	GO:0015267	channel activity	Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
	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: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:0008053	mitochondrial fusion	Merging of two or more mitochondria within a cell to form a single compartment.
	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:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	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:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.

Chain B (APR_HUMAN | Q13794)

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:0043029	T cell homeostasis	The process of regulating the proliferation and elimination of T cells such that the total number of T cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
	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: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:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0042149	cellular response to glucose starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of glucose.
	GO:0071456	cellular response to hypoxia	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0097193	intrinsic apoptotic signaling pathway	A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	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 cell cycle regulator phosphoprotein p53, or an equivalent protein, 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:0042771	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	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 cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
	GO:0048147	negative regulation of fibroblast proliferation	Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	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:0043517	positive regulation of DNA damage response, signal transduction by p53 class mediator	Any process that activates, maintains or increases the rate of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
	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:0043280	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
	GO:1902237	positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
	GO:1902043	positive regulation of extrinsic apoptotic signaling pathway via death domain receptors	Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
	GO:0010907	positive regulation of glucose metabolic process	Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
	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:0043525	positive regulation of neuron apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
	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:0010498	proteasomal protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
	GO:0001844	protein insertion into mitochondrial membrane involved in apoptotic signaling pathway	The process in which a protein is incorporated into a mitochondrial membrane as the initial phase of the mitochondrial membrane permeabilization that takes place in the apoptotic signaling pathway.
	GO:0072593	reactive oxygen species metabolic process	The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0046902	regulation of mitochondrial membrane permeability	Any process that modulates the frequency, rate or extent of the passage or uptake of molecules by the mitochondrial membrane.
	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:0009411	response to UV	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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0010165	response to X-ray	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 X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
	GO:0043331	response to dsRNA	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 a double-stranded RNA stimulus.
cellular component
	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: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.
	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.

Asymmetric/Biological Unit
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	B2LA1_HUMAN \| Q16548
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UniProtKB/Swiss-Prot
	B2LA1_HUMAN \| Q16548	:	2vm6 3i1h 4zeq 5uuk 5uul 5uup

3i1h	THE SAME HUMAN BFL-1 IN COMPLEX WITH A DIFFERENT BCL-2 BH3 PEPTIDE RELATED ID: HR2930 RELATED DB: TARGETDB

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Ligands, Modified Residues, Ions (0, 0)

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