1SHX - JenaLib

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Title :   EPHRIN A5 LIGAND STRUCTURE

Authors :   J. P. Himanen, W. A. Barton, D. B. Nikolov, P. D. Jeffrey

Date :   26 Feb 04 (Deposition) - 19 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

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

Reference :   B. Day, C. To, J. P. Himanen, F. M. Smith, D. B. Nikolov, A. W. Boyd, M. Lackmann
Three Distinct Molecular Surfaces In Ephrin-A5 Are Essentia For A Functional Interaction With Epha3.
J. Biol. Chem. V. 280 26526 2005
PubMed-ID: 15901737 | Reference-DOI: 10.1074/JBC.M504972200
(for further references see the PDB file header)

Molecule 1 - EPHRIN-A5
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Common	:	HUMAN
	Expression System Organ	:	KIDNEY
	Expression System Taxid	:	9606
	Gene	:	EFNA5, EPLG7, LERK7, EPL7
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 7, LERK-7, AL-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:39 , ASN A:41 , PRO A:67 , HIS A:68 , TYR A:69 , NAG A:402 , HOH A:414 , HOH A:429 , HOH A:430 , HOH A:460	BINDING SITE FOR RESIDUE NAG A 401
2	AC2	SOFTWARE	TYR A:39 , NAG A:401 , NAG A:403	BINDING SITE FOR RESIDUE NAG A 402
3	AC3	SOFTWARE	TYR A:39 , NAG A:402 , HOH A:416 , HOH A:432 , HOH A:433 , HOH A:441	BINDING SITE FOR RESIDUE NAG A 403
4	AC4	SOFTWARE	TYR B:39 , ASN B:41 , ASN B:44 , PRO B:67 , HIS B:68 , TYR B:69 , NAG B:502 , HOH B:509 , HOH B:536	BINDING SITE FOR RESIDUE NAG B 501
5	AC5	SOFTWARE	NAG B:501 , HOH B:543	BINDING SITE FOR RESIDUE NAG B 502

Asymmetric Unit

No.	Residues
1	A:57	-	A:169
2	A:66	-	A:106
3	A:94	-	A:156
4	B:57	-	B:169
5	B:66	-	B:106
6	B:94	-	B:156

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EPHRIN_RBD_2	PS51551	Ephrin receptor-binding (ephrin RBD) domain profile.	EFNA5_MOUSE	29-162	2	A:33-167 B:33-167
2	EPHRIN_RBD_1	PS01299	Ephrin receptor-binding (ephrin RBD) domain signature.	EFNA5_MOUSE	113-140	2	A:117-144 B:117-144

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EPHRIN_RBD_2	PS51551	Ephrin receptor-binding (ephrin RBD) domain profile.	EFNA5_MOUSE	29-162	1	A:33-167 -
2	EPHRIN_RBD_1	PS01299	Ephrin receptor-binding (ephrin RBD) domain signature.	EFNA5_MOUSE	113-140	1	A:117-144 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EPHRIN_RBD_2	PS51551	Ephrin receptor-binding (ephrin RBD) domain profile.	EFNA5_MOUSE	29-162	1	- B:33-167
2	EPHRIN_RBD_1	PS01299	Ephrin receptor-binding (ephrin RBD) domain signature.	EFNA5_MOUSE	113-140	1	- B:117-144

(no "Exon" information available for 1SHX)

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:138
 aligned with EFNA5_MOUSE | O08543 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:138
                                    37        47        57        67        77        87        97       107       117       127       137       147       157        
          EFNA5_MOUSE    28 VADRYAVYWNSSNPRFQRGDYHIDVCINDYLDVFCPHYEDSVPEDKTERYVLYMVNFDGYSACDHTSKGFKRWECNRPHSPNGPLKFSEKFQLFTPFSLGFEFRPGREYFYISSAIPDNGRRSCLKLKVFVRPTNSCM 165
               SCOP domains d1shxa_ A: Ephrin-a5                                                                                                                       SCOP domains
               CATH domains 1shxA00 A:32-170 Cupredoxins -  blue copper proteins                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhhh...eeee....eeeee...............eeeeeehhhhhhh......eeeeeee..........eeeee................eeeeeeeee..........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -EPHRIN_RBD_2  PDB: A:33-167 UniProt: 29-162                                                                                           --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------EPHRIN_RBD_1  PDB: A:117-144------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1shx A  32 VADRYAVYWNSSNPRFQRGDYHIDVCINDYLDVFCPHYEDSVPEDKTERYVLYMVNFDGYSACDHTSKGFKRWECNRPHSPNGPLKFSEKFQLFTPFSLGFEFRPGREYFYISSAIPDNGRRSCLKLKVFVRPTNSCM 170
                                    41        51        61        71        81        91       101       111       121       131       141      |152       162        
                                                                                                                                              148|                    
                                                                                                                                               150

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with EFNA5_MOUSE | O08543 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:138
                                    37        47        57        67        77        87        97       107       117       127       137       147       157        
          EFNA5_MOUSE    28 VADRYAVYWNSSNPRFQRGDYHIDVCINDYLDVFCPHYEDSVPEDKTERYVLYMVNFDGYSACDHTSKGFKRWECNRPHSPNGPLKFSEKFQLFTPFSLGFEFRPGREYFYISSAIPDNGRRSCLKLKVFVRPTNSCM 165
               SCOP domains d1shxb_ B: Ephrin-a5                                                                                                                       SCOP domains
               CATH domains 1shxB00 B:32-170 Cupredoxins -  blue copper proteins                                                                                       CATH domains
           Pfam domains (1) Ephrin-1shxB01 B:32-169                                                                                                                  - Pfam domains (1)
           Pfam domains (2) Ephrin-1shxB02 B:32-169                                                                                                                  - Pfam domains (2)
         Sec.struct. author ...eeeee....hhhhhh...eeee....eeeee...............eeeeeehhhhhhhh.....eeeeeee..........eeeee................eeeeeeeee..........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -EPHRIN_RBD_2  PDB: B:33-167 UniProt: 29-162                                                                                           --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------EPHRIN_RBD_1  PDB: B:117-144------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1shx B  32 VADRYAVYWNSSNPRFQRGDYHIDVCINDYLDVFCPHYEDSVPEDKTERYVLYMVNFDGYSACDHTSKGFKRWECNRPHSPNGPLKFSEKFQLFTPFSLGFEFRPGREYFYISSAIPDNGRRSCLKLKVFVRPTNSCM 170
                                    41        51        61        71        81        91       101       111       121       131       141      |152       162        
                                                                                                                                              148|                    
                                                                                                                                               150

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: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Ephrin ectodomain (11)

Protein domain: Ephrin-a5 (2)

Mouse (Mus musculus) [TaxId: 10090] (2)

1a	d1shxa_	A:
1b	d1shxb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

House mouse (Mus musculus) (4)

1a	1shxA00	A:32-170
1b	1shxB00	B:32-170

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Ephrin (10)

Mus musculus (Mouse) (3)

1a	Ephrin-1shxB01	B:32-169
1b	Ephrin-1shxB02	B:32-169

Asymmetric Unit(hide GO term definitions)

Chain A,B (EFNA5_MOUSE | O08543)

molecular function
	GO:0045499	chemorepellent activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal.
	GO:0046875	ephrin receptor binding	Interacting selectively and non-covalently with an ephrin receptor.
	GO:0005169	neurotrophin TRKB receptor binding	Interacting selectively and non-covalently with the neurotrophin TRKB 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).
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:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0071372	cellular response to follicle-stimulating hormone 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 follicle-stimulating hormone stimulus.
	GO:1904322	cellular response to forskolin	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 forskolin stimulus.
	GO:0048668	collateral sprouting	The process in which outgrowths develop from the shafts of existing axons.
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	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:0050919	negative chemotaxis	The directed movement of a motile cell or organism towards a lower concentration of a chemical.
	GO:1900025	negative regulation of substrate adhesion-dependent cell spreading	Any process that stops, prevents or reduces the frequency, rate or extent of substrate adhesion-dependent cell spreading.
	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:0048672	positive regulation of collateral sprouting	Any process that activates or increases the frequency, rate or extent of collateral sprouting.
	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: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:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0032956	regulation of actin cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0022604	regulation of cell morphogenesis	Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized.
	GO:0022407	regulation of cell-cell adhesion	Any process that modulates the frequency, rate or extent of attachment of a cell to another cell.
	GO:0051893	regulation of focal adhesion assembly	Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions.
	GO:0061178	regulation of insulin secretion involved in cellular response to glucose stimulus	Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
	GO:0070507	regulation of microtubule cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
	GO:0031290	retinal ganglion cell axon guidance	The process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
cellular component
	GO:0005912	adherens junction	A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
	GO:0031362	anchored component of external side of plasma membrane	The component of the plasma membrane consisting of the gene products that are tethered to the external side of the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0046658	anchored component of plasma membrane	The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0005604	basement membrane	A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
	GO:0005901	caveola	A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
	GO:0071944	cell periphery	The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
	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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