3N1G - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DHHN BOUND TO BOCFN3

Authors :   J. M. Kavran, D. J. Leahy

Date :   15 May 10 (Deposition) - 02 Jun 10 (Release) - 16 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Binding Sites, Calcium, Cell Adhesion Molecules, Cell Cycle Proteins, Cell Line, Conserved Sequence, Fibronectins, Hedgehog Proteins, Immunoglobulin G, Membrane Glycoproteins, Membrane Proteins, Protein Binding, Tertiary, Receptors, Cell Surface, Sequence Homology, Signal Transduction, Tumor Suppressor Proteins (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Kavran, M. D. Ward, O. O. Oladosu, S. Mulepati, D. J. Leahy
All Mammalian Hedgehog Proteins Interact With Cdo And Boc In A Conserved Manner.
J. Biol. Chem. 2010
PubMed-ID: 20519495 | Reference-DOI: 10.1074/JBC.M110.131680

Molecule 1 - DESERT HEDGEHOG PROTEIN
	Chains	:	B, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DHH
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DHH, HHG-3, DESERT HEDGEHOG PROTEIN N-PRODUCT, DESERT HEDGEHOG PROTEIN C-PRODUCT

Molecule 2 - BROTHER OF CDO
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BOC, UNQ604/PRO1190
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN BOC

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:		B	C
Biological Unit 2 (1x)	:	A			D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:7 , HOH B:15 , GLU B:91 , GLU B:127 , ASP B:130 , ASP B:132 , HOH B:209	BINDING SITE FOR RESIDUE CA B 190
2	AC2	SOFTWARE	GLU B:90 , GLU B:91 , ASP B:96 , THR B:126 , GLU B:127	BINDING SITE FOR RESIDUE CA B 191
3	AC3	SOFTWARE	HIS B:141 , ASP B:148 , GLU B:177 , HIS B:183 , HOH B:278 , HOH B:510	BINDING SITE FOR RESIDUE ZN B 192
4	AC4	SOFTWARE	HOH A:8 , HOH A:14 , HOH A:16 , GLU A:91 , GLU A:127 , ASP A:130 , ASP A:132	BINDING SITE FOR RESIDUE CA A 190
5	AC5	SOFTWARE	HIS A:141 , ASP A:148 , GLU A:177 , HIS A:183 , HOH A:305	BINDING SITE FOR RESIDUE ZN A 191
6	AC6	SOFTWARE	GLU A:90 , GLU A:91 , ASP A:96 , THR A:126 , GLU A:127	BINDING SITE FOR RESIDUE CA A 192
7	AC7	SOFTWARE	THR A:100 , ARG A:102 , VAL A:186 , LYS A:187 , ALA A:188 , ASP A:189	BINDING SITE FOR RESIDUE MG A 193

(no "SS Bond" information available for 3N1G)

Asymmetric Unit

No.	Residues
1	Val B:49	-	Pro B:50
2	Gln A:39	-	Leu A:40
3	Val A:49	-	Pro A:50

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_054873	L	162	P	DHH_HUMAN	Disease (SRXY7)	111033589	A/B	L	162	P
2	UniProt	VAR_035503	V	713	M	BOC_HUMAN	Unclassified	367589886	C/D	V	713	M
3	CancerSNP	VAR_BOC_HUMAN_CCDS2971_1_01 *	V	713	M	BOC_HUMAN	Disease (Breast cancer)	---	C/D	V	713	M
	* ID not provided by source

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_054873	L	162	P	DHH_HUMAN	Disease (SRXY7)	111033589	B	L	162	P
2	UniProt	VAR_035503	V	713	M	BOC_HUMAN	Unclassified	367589886	C	V	713	M
3	CancerSNP	VAR_BOC_HUMAN_CCDS2971_1_01 *	V	713	M	BOC_HUMAN	Disease (Breast cancer)	---	C	V	713	M
	* ID not provided by source

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_054873	L	162	P	DHH_HUMAN	Disease (SRXY7)	111033589	A	L	162	P
2	UniProt	VAR_035503	V	713	M	BOC_HUMAN	Unclassified	367589886	D	V	713	M
3	CancerSNP	VAR_BOC_HUMAN_CCDS2971_1_01 *	V	713	M	BOC_HUMAN	Disease (Breast cancer)	---	D	V	713	M
	* ID not provided by source

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FN3	PS50853	Fibronectin type-III domain profile.	BOC_HUMAN	474-571 608-703 712-812	2	- - C:712-812 D:712-812

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FN3	PS50853	Fibronectin type-III domain profile.	BOC_HUMAN	474-571 608-703 712-812	1	- - C:712-812 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FN3	PS50853	Fibronectin type-III domain profile.	BOC_HUMAN	474-571 608-703 712-812	1	- - - D:712-812

(no "Exon" information available for 3N1G)

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:151
 aligned with DHH_HUMAN | O43323 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:151
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188 
            DHH_HUMAN    39 QLVPLLYKQFVPGVPERTLGASGPAEGRVARGSERFRDLVPNYNPDIIFKDEENSGADRLMTERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHVHVSVKAD 189
               SCOP domains d3n1ga_ A: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.....................hhhhhh.ee.....eee......hhh.eehhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhh.eeeeee...hhhhhhhhhhhhhhh...eee......eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------P--------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n1g A  39 QLVPLLYKQFVPGVPERTLGASGPAEGRVARGSERFRDLVPNYNPDIIFKDEENSGADRLMTERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHVHVSVKAD 189
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with DHH_HUMAN | O43323 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:151
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188 
            DHH_HUMAN    39 QLVPLLYKQFVPGVPERTLGASGPAEGRVARGSERFRDLVPNYNPDIIFKDEENSGADRLMTERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHVHVSVKAD 189
               SCOP domains d3n1gb_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) HH_signal-3n1gB01 B:39-185                                                                                                                         ---- Pfam domains (1)
           Pfam domains (2) HH_signal-3n1gB02 B:39-185                                                                                                                         ---- Pfam domains (2)
         Sec.struct. author .........ee.....................hhhhhh.ee.....eee......hhh.eehhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhh.eeeeee...hhhhhhhhhhhhhhh...eee......eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------P--------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n1g B  39 QLVPLLYKQFVPGVPERTLGASGPAEGRVARGSERFRDLVPNYNPDIIFKDEENSGADRLMTERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHVHVSVKAD 189
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with BOC_HUMAN | Q9BWV1 from UniProtKB/Swiss-Prot  Length:1114

    Alignment length:104
                                   719       729       739       749       759       769       779       789       799       809    
            BOC_HUMAN   710 ERPVAGPYITFTDAVNETTIMLKWMYIPASNNNTPIHGFYIYYRPTDSDNDSDYKKDMVEGDKYWHSISHLQPETSYDIKMQCFNEGGESEFSNVMICETKARK 813
               SCOP domains d3n1gc_ C: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee..eeeeeee.hhhhhh.....eeeeeeee....hhhhheeeeee....eeee.......eeeeeeeee...........eeee..... Sec.struct. author
             SAPs(SNPs) (1) ---M---------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---M---------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --FN3  PDB: C:712-812 UniProt: 712-812                                                                 - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3n1g C 710 ERPVAGPYITFTDAVNETTIMLKWMYIPASNNNTPIHGFYIYYRPTDSDNDSDYKKDMVEGDKYWHSISHLQPETSYDIKMQCFNEGGESEFSNVMICETKARK 813
                                   719       729       739       749       759       769       779       789       799       809

Chain D from PDB  Type:PROTEIN  Length:99
 aligned with BOC_HUMAN | Q9BWV1 from UniProtKB/Swiss-Prot  Length:1114

    Alignment length:104
                                   719       729       739       749       759       769       779       789       799       809    
            BOC_HUMAN   710 ERPVAGPYITFTDAVNETTIMLKWMYIPASNNNTPIHGFYIYYRPTDSDNDSDYKKDMVEGDKYWHSISHLQPETSYDIKMQCFNEGGESEFSNVMICETKARK 813
               SCOP domains d3n1gd_ D: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------fn3-3n1gD01 D:716-802                                                                  ----------- Pfam domains (1)
           Pfam domains (2) ------fn3-3n1gD02 D:716-802                                                                  ----------- Pfam domains (2)
         Sec.struct. author .......eeeeeee.....eeeeee...-----....eeeeeeee....hhhhheeeeee....eeee.......eeeeeeeee...........eeee..... Sec.struct. author
             SAPs(SNPs) (1) ---M---------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---M---------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --FN3  PDB: D:712-812 UniProt: 712-812                                                                 - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3n1g D 710 ERPVAGPYITFTDAVNETTIMLKWMYIP-----TPIHGFYIYYRPTDSDNDSDYKKDMVEGDKYWHSISHLQPETSYDIKMQCFNEGGESEFSNVMICETKARK 813
                                   719       729       | -   |   749       759       769       779       789       799       809    
                                                     737   743

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 3N1G)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: fn3 (66)

Homo sapiens (Human) (52)

1a	fn3-3n1gD01	D:716-802
1b	fn3-3n1gD02	D:716-802

Clan: Peptidase_MD (20)

Family: HH_signal (16)

Homo sapiens (Human) (13)

2a	HH_signal-3n1gB01	B:39-185
2b	HH_signal-3n1gB02	B:39-185

Asymmetric Unit(hide GO term definitions)

Chain A,B (DHH_HUMAN | O43323)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005113	patched binding	Interacting selectively and non-covalently with the patched (ptc) protein, a receptor for hedgehog proteins.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0033327	Leydig cell differentiation	The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a Leydig cell. A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
	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:0030238	male sex determination	The specification of male sex of an individual organism.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0050810	regulation of steroid biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	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:0043627	response to estrogen	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 an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
	GO:0007286	spermatid development	The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
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.
	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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D (BOC_HUMAN | Q9BWV1)

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: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:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0098779	positive regulation of macromitophagy in response to mitochondrial depolarization	The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
	GO:0051149	positive regulation of muscle cell differentiation	Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
	GO:0045663	positive regulation of myoblast differentiation	Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
	GO:0007224	smoothened signaling pathway	A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
cellular component
	GO:0044295	axonal growth cone	The migrating motile tip of a growing nerve cell axon.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes 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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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		Gln A:39 - Leu A:40	[ RasMol ]
		Val A:49 - Pro A:50	[ RasMol ]
		Val B:49 - Pro B:50	[ RasMol ]

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UniProtKB/Swiss-Prot
	BOC_HUMAN \| Q9BWV1	:	3n1m 3n1p
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

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