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Title :   STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER

Authors :   R. C. Robinson, C. Radziejewski, D. I. Stuart, E. Y. Jones

Date :   12 Dec 94 (Deposition) - 04 Apr 96 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Neurotrophin, Complex (Growth Factor-Growth Factor) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. C. Robinson, C. Radziejewski, D. I. Stuart, E. Y. Jones
Structure Of The Brain-Derived Neurotrophic Factor/Neurotrophin 3 Heterodimer.
Biochemistry V. 34 4139 1995
PubMed-ID: 7703225 | Reference-DOI: 10.1021/BI00013A001
(for further references see the PDB file header)

Molecule 1 - BRAIN DERIVED NEUROTROPHIC FACTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organ	:	BRAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	SUPPLIED BY REGENERON PHARM.
	Synonym	:	BDNF

Molecule 2 - NEUROTROPHIN 3
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organ	:	BRAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	HETERODIMER
	Other Details - Source	:	SUPPLIED BY REGENERON PHARM.
	Synonym	:	NT3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:29 , ASP A:30 , GLY A:33 , TYR A:86 , ARG A:104 , VAL B:11 , ARG B:68	BINDING SITE FOR RESIDUE IPA A 500

Asymmetric Unit

No.	Residues
1	A:13	-	A:80
2	A:58	-	A:109
3	A:68	-	A:111
4	B:14	-	B:79
5	B:57	-	B:108
6	B:67	-	B:110

Asymmetric Unit

No.	Residues
1	Ser B:46	-	Pro B:47

(no "SAP(SNP)/Variant" information available for 1BND)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NGF_1	PS00248	Nerve growth factor family signature.	BDNF_HUMAN	195-208	1	A:67-80
1	NGF_1	PS00248	Nerve growth factor family signature.	NTF3_HUMAN	204-217	1	B:66-79

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NGF_1	PS00248	Nerve growth factor family signature.	BDNF_HUMAN	195-208	2	A:67-80
1	NGF_1	PS00248	Nerve growth factor family signature.	NTF3_HUMAN	204-217	2	B:66-79

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NGF_1	PS00248	Nerve growth factor family signature.	BDNF_HUMAN	195-208	1	A:67-80
1	NGF_1	PS00248	Nerve growth factor family signature.	NTF3_HUMAN	204-217	1	B:66-79

Asymmetric Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000331010	2a	ENSE00001740540	chr12:5603311-5604344	1034	NTF3_HUMAN	1-281	281	1	B:8-116 (gaps)	109

2.5	ENST00000395983	5	ENSE00001593506	chr11:27722600-27722518	83	BDNF_HUMAN	-	0	0	-	-
2.11f	ENST00000395983	11f	ENSE00002153606	chr11:27680132-27676440	3693	BDNF_HUMAN	1-254	254	1	A:8-116	109

Asymmetric Unit

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Chain A from PDB  Type:PROTEIN  Length:109
 aligned with BDNF_HUMAN | P23560 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:109
                                   145       155       165       175       185       195       205       215       225       235         
           BDNF_HUMAN   136 GELSVCDSISEWVTAADKKTAVDMSGGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRALTMDSKKRIGWRFIRIDTSCVCTLTIK 244
               SCOP domains d1bnda_ A: Brain-derived neurotrophic factor, BDNF                                                            SCOP domains
               CATH domains 1bndA00 A:8-116 Cystine-knot cytokines                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeehhhh.eee.....eee...eee....eee.eeeeeee....hhh..........eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------NGF_1         ------------------------------------ PROSITE
               Transcript 2 Exon 2.11f  PDB: A:8-116 UniProt: 1-254 [INCOMPLETE]                                                          Transcript 2
                 1bnd A   8 GQLSVCDSISEWVTAADKKTAVDMSGGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRALTMDSKKRIGWRFIRIDTSCVCTLTIK 116
                                    17        27        37        47        57        67        77        87        97       107

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with NTF3_HUMAN | P20783 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:108
                                   155       165       175       185       195       205       215       225       235       245        
           NTF3_HUMAN   146 RGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRK 253
               SCOP domains d1bndb_ B: Neurotrophin 3, NT3                                                                               SCOP domains
               CATH domains 1bndB00 B:8-116 Cystine-knot cytokines                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...eeeeee....eee.....eee...............eeeeee..................eeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------NGF_1         ------------------------------------ PROSITE (2)
               Transcript 1 Exon 1.2a  PDB: B:8-116 (gaps) UniProt: 1-281 [INCOMPLETE]                                                   Transcript 1
                 1bnd B   8 RGEVSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTQNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRK 116
                                    17        27        37        47        57        67        77        87        97       107      ||
                                                                                                                                    114|
                                                                                                                                     116

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Small proteins (3458)

Fold: Cystine-knot cytokines (124)

Superfamily: Cystine-knot cytokines (124)

Family: Neurotrophin (20)

Protein domain: Brain-derived neurotrophic factor, BDNF (2)

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

d1bnda_

Protein domain: Neurotrophin 3, NT3 (3)

Human (Homo sapiens) [TaxId: 9606] (3)

d1bndb_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Cystine Knot Cytokines, subunit B (102)

Homologous Superfamily: Cystine-knot cytokines (102)

Human (Homo sapiens) (84)

1a	1bndB00	B:8-116
1b	1bndA00	A:8-116

(no "Pfam Domain" information available for 1BND)

Asymmetric Unit(hide GO term definitions)

Chain A (BDNF_HUMAN | P23560)

molecular function
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0005169	neurotrophin TRKB receptor binding	Interacting selectively and non-covalently with the neurotrophin TRKB receptor.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0031547	brain-derived neurotrophic factor receptor signaling pathway	The series of molecular signals generated as a consequence of a brain-derived neurotrophic factor receptor binding to one of its physiological ligands.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0048668	collateral sprouting	The process in which outgrowths develop from the shafts of existing axons.
	GO:0043524	negative regulation of neuron apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0031550	positive regulation of brain-derived neurotrophic factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of signaling via the brain-derived neurotrophic factor receptor signaling pathway.
	GO:0048672	positive regulation of collateral sprouting	Any process that activates or increases the frequency, rate or extent of collateral sprouting.
	GO:0051965	positive regulation of synapse assembly	Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
	GO:0007416	synapse assembly	The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Chain B (NTF3_HUMAN | P20783)

molecular function
	GO:0042056	chemoattractant activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0048406	nerve growth factor binding	Interacting selectively and non-covalently with nerve growth factor (NGF).
	GO:0005166	neurotrophin p75 receptor binding	Interacting selectively and non-covalently with the neurotrophin p75 receptor.
	GO:0005165	neurotrophin receptor binding	Interacting selectively and non-covalently with a neurotrophin receptor.
	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:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0090630	activation of GTPase activity	Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0032148	activation of protein kinase B activity	Any process that initiates the activity of the inactive enzyme protein kinase B.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0050930	induction of positive chemotaxis	Any process that initiates the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
	GO:0050804	modulation of chemical synaptic transmission	Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
	GO:0042552	myelination	The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
	GO:0043524	negative regulation of neuron apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
	GO:0050732	negative regulation of peptidyl-tyrosine phosphorylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0048812	neuron projection morphogenesis	The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
	GO:0050918	positive chemotaxis	The directed movement of a motile cell or organism towards a higher concentration of a chemical.
	GO:2000251	positive regulation of actin cytoskeleton reorganization	Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0045687	positive regulation of glial cell differentiation	Any process that activates or increases the frequency, rate or extent of glia cell differentiation.
	GO:0033138	positive regulation of peptidyl-serine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0002092	positive regulation of receptor internalization	Any process that activates or increases the frequency, rate or extent of receptor internalization.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0045664	regulation of neuron differentiation	Any process that modulates the frequency, rate or extent of neuron differentiation.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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