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Title :   CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHANISMS OF MEMBRANE PERMEABILIZATION

Authors :   C. P. Hill, J. Yee, M. E. Selsted, D. Eisenberg

Date :   18 Jan 91 (Deposition) - 15 Jul 92 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Defensin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. P. Hill, J. Yee, M. E. Selsted, D. Eisenberg
Crystal Structure Of Defensin Hnp-3, An Amphiphilic Dimer: Mechanisms Of Membrane Permeabilization.
Science V. 251 1481 1991
PubMed-ID: 2006422
(for further references see the PDB file header)

Molecule 1 - DEFENSIN HNP-3
	Chains	:	A, B
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1DFN)

Asymmetric Unit

No.	Residues
1	A:3	-	A:31
2	A:5	-	A:20
3	A:10	-	A:30
4	B:3	-	B:31
5	B:5	-	B:20
6	B:10	-	B:30

Asymmetric Unit

No.	Residues
1	Ile A:7	-	Pro A:8
2	Ile B:7	-	Pro B:8

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF3_HUMAN	66-94	2	A:3-31 B:3-31
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF1_HUMAN	66-94	2	A:3-31 B:3-31

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF3_HUMAN	66-94	2	A:3-31 B:3-31
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF1_HUMAN	66-94	2	A:3-31 B:3-31

Biological Unit 2 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF3_HUMAN	66-94	4	A:3-31 B:3-31
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF1_HUMAN	66-94	4	A:3-31 B:3-31

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000327857	1	ENSE00001493010	chr8:6875823-6875744	80	DEF3_HUMAN	-	0	0	-	-
1.2	ENST00000327857	2	ENSE00001719742	chr8:6874384-6874198	187	DEF3_HUMAN	1-59	59	0	-	-
1.3	ENST00000327857	3	ENSE00001306731	chr8:6873621-6873391	231	DEF3_HUMAN	59-94	36	2	A:2-31 B:2-31	30 30

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:30
 aligned with DEF1_HUMAN | P59665 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:30
                                    74        84        94
            DEF1_HUMAN   65 ACYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains d1dfna_ A: Defensin HNP-3      SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE -DEFENSIN  PDB: A:3-31         PROSITE
                 Transcript ------------------------------ Transcript
                  1dfn A  2 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 31
                                    11        21        31

Chain A from PDB  Type:PROTEIN  Length:30
 aligned with DEF3_HUMAN | P59666 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:30
                                    74        84        94
            DEF3_HUMAN   65 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains d1dfna_ A: Defensin HNP-3      SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                PROSITE (2) -DEFENSIN  PDB: A:3-31         PROSITE (2)
               Transcript 1 Exon 1.3  PDB: A:2-31          Transcript 1
                  1dfn A  2 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 31
                                    11        21        31

Chain B from PDB  Type:PROTEIN  Length:30
 aligned with DEF1_HUMAN | P59665 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:30
                                    74        84        94
            DEF1_HUMAN   65 ACYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains d1dfnb_ B: Defensin HNP-3      SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE -DEFENSIN  PDB: B:3-31         PROSITE
                 Transcript ------------------------------ Transcript
                  1dfn B  2 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 31
                                    11        21        31

Chain B from PDB  Type:PROTEIN  Length:30
 aligned with DEF3_HUMAN | P59666 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:30
                                    74        84        94
            DEF3_HUMAN   65 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains d1dfnb_ B: Defensin HNP-3      SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                PROSITE (2) -DEFENSIN  PDB: B:3-31         PROSITE (2)
               Transcript 1 Exon 1.3  PDB: B:2-31          Transcript 1
                  1dfn B  2 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 31
                                    11        21        31

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: Small proteins (3458)

Fold: Defensin-like (59)

Superfamily: Defensin-like (59)

Family: Defensin (50)

Protein domain: Defensin HNP-3 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1dfna_	A:
1b	d1dfnb_	B:

(no "CATH Domain" information available for 1DFN)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (DEF1_HUMAN | P59665)

biological process
	GO:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	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:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0002227	innate immune response in mucosa	Any process of the innate immune response that takes place in the mucosal tissues.
	GO:0030520	intracellular estrogen receptor signaling pathway	Any series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription).
	GO:0031640	killing of cells of other organism	Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
cellular component
	GO:0005796	Golgi lumen	The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
	GO:0035578	azurophil granule lumen	The volume enclosed by the membrane of an azurophil granule, a primary lysosomal granule found in neutrophil granulocytes that contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
	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:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Chain A,B (DEF3_HUMAN | P59666)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	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:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0002227	innate immune response in mucosa	Any process of the innate immune response that takes place in the mucosal tissues.
	GO:0030520	intracellular estrogen receptor signaling pathway	Any series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription).
	GO:0031640	killing of cells of other organism	Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
cellular component
	GO:0005796	Golgi lumen	The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
	GO:0035578	azurophil granule lumen	The volume enclosed by the membrane of an azurophil granule, a primary lysosomal granule found in neutrophil granulocytes that contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
	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: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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 1dfn)

	Cis Peptide Bonds
		Ile A:7 - Pro A:8	[ RasMol ]
		Ile B:7 - Pro B:8	[ RasMol ]

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	1dfn
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	DEF1_HUMAN \| P59665
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	DEF3_HUMAN \| P59666
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(no "Related Entries Specified in the PDB File" available for 1DFN)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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Exons (1, 2)

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Gene Ontology (19, 34)

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