1NPE - JenaLib

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Title :   CRYSTAL STRUCTURE OF NIDOGEN/LAMININ COMPLEX

Authors :   J. Takagi, Y. T. Yang, J. -H. Liu, J. -H. Wang, T. A. Springer

Date :   17 Jan 03 (Deposition) - 12 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Glycoprotein, Basement Membrane, Beta-Propeller, Egf-Like, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Takagi, Y. T. Yang, J. -H. Liu, J. -H. Wang, T. A. Springer
Complex Between Nidogen And Laminin Fragments Reveals A Paradigmatic Beta-Propeller Interface
Nature V. 424 969 2003
PubMed-ID: 12931195 | Reference-DOI: 10.1038/NATURE01873
(for further references see the PDB file header)

Molecule 1 - NIDOGEN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	293-EBNA
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PCEP-PU
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	G3 YWTD DOMAIN, SEQUENCE DATABASE RESIDUE 941- 1203
	Gene	:	NID OR NID1 OR ENT
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	ENTACTIN

Molecule 2 - LAMININ GAMMA-1 CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	293-EBNA
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PCEP4
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	MODULES III 3-5, SEQUENCE DATABASE RESIDUE 769- 932
	Gene	:	LAMC1
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	LAMININ B2 CHAIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	CD	6	Ligand/Ion	CADMIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:3 , HOH A:23 , HOH A:25 , SER A:1010 , ASP A:1013 , VAL A:1034	BINDING SITE FOR RESIDUE CD A 5001
2	AC2	SOFTWARE	HIS A:1064 , ASP A:1066 , THR A:1068 , HOH B:89 , GLU B:831 , SER B:862	BINDING SITE FOR RESIDUE CD B 5002
3	AC3	SOFTWARE	HOH A:94 , HOH A:108 , HIS A:1101	BINDING SITE FOR RESIDUE CD A 5003
4	AC4	SOFTWARE	HOH A:84 , HIS A:1160 , HIS B:759	BINDING SITE FOR RESIDUE CD B 5004
5	AC5	SOFTWARE	HOH A:102 , HIS A:944 , GLU B:754	BINDING SITE FOR RESIDUE CD A 5005
6	AC6	SOFTWARE	HOH B:105 , HOH B:106 , HIS B:875	BINDING SITE FOR RESIDUE CD B 5006

Asymmetric/Biological Unit

No.	Residues
1	A:957	-	A:1175
2	A:1094	-	A:1105
3	B:738	-	B:746
4	B:740	-	B:757
5	B:760	-	B:769
6	B:772	-	B:790
7	B:793	-	B:807
8	B:795	-	B:814
9	B:817	-	B:826
10	B:829	-	B:846
11	B:849	-	B:863
12	B:851	-	B:870
13	B:872	-	B:881
14	B:884	-	B:897

Asymmetric/Biological Unit

No.	Residues
1	Glu A:969	-	Pro A:970

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

Asymmetric/Biological Unit (4, 11)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_LAM_2	PS50027	Laminin-type EGF-like (LE) domain profile.	LAMC1_MOUSE	284-329 340-395 396-442 443-492 722-770 771-825 826-881 882-932 933-980 981-1028	3	- - - - - B:738-792 B:793-848 B:849-899 - -
2	EGF_1	PS00022	EGF-like domain signature 1.	LAMC1_MOUSE	303-314 414-425 461-472 688-699 738-749 903-914 952-963 999-1010	1	- - - - - B:870-881 - -
3	EGF_LAM_1	PS01248	Laminin-type EGF-like (LE) domain signature.	LAMC1_MOUSE	365-398 414-445 461-495 688-722 738-773 790-826 847-882 903-935 952-983 999-1032	3	- - - - - B:757-793 B:814-849 B:870-899 - -
4	LDLRB	PS51120	LDL-receptor class B (LDLRB) repeat profile.	NID1_MOUSE	988-1030 1031-1073 1074-1118 1119-1160	4	A:960-1002 A:1003-1045 A:1046-1090 A:1091-1132

(no "Exon" information available for 1NPE)

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:263
 aligned with NID1_MOUSE | P10493 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:263
                                   950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200   
          NID1_MOUSE    941 GTHLLFAQTGKIERLPLERNTMKKTEAKAFLHIPAKVIIGLAFDCVDKVVYWTDISEPSIGRASLHGGEPTTIIRQDLGSPEGIALDHLGRTIFWTDSQLDRIEVAKMDGTQRRVLFDTGLVNPRGIVTDPVRGNLYWTDWNRDNPKIETSHMDGTNRRILAQDNLGLPNGLTFDAFSSQLCWVDAGTHRAECLNPAQPGRRKVLEGLQYPFAVTSYGKNLYYTDWKTNSVIAMDLAISKEMDTFHPHKQTRLYGITIALSQC 1203
               SCOP domains d1npea_ A: Nidogen                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1npeA00 A:913-1175 TolB, C-terminal domain                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------Ldl_recept_b-1npeA01 A:1046-1088           --------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------Ldl_recept_b-1npeA02 A:1046-1088           --------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------Ldl_recept_b-1npeA03 A:1046-1088           --------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .eeeeeeeeeeeeeeee.....hhhhheeeeeeeeeeeeeeeee....eeeeee....eeeeee......eeee......eeeeeee....eeeeee....eeeeee......eeee......eeeeeee....eeeeee......eeeeee......eeee......eeeeeee....eeeeee....eeeeee..eeeeeeeee....eeeeeee..eeeeee....eeeeee....eeeeee..........eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------LDLRB  PDB: A:960-1002 UniProt: 988-1030   LDLRB  PDB: A:1003-1045 UniProt: 1031-1073 LDLRB  PDB: A:1046-1090 UniProt: 1074-1118   LDLRB  PDB: A:1091-1132 UniProt: 1119-1160------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1npe A  913 GTHLLFAQTGKIERLPLERNTMKKTEAKAFLHIPAKVIIGLAFDCVDKVVYWTDISEPSIGRASLHGGEPTTIIRQDLGSPEGIALDHLGRTIFWTDSQLDRIEVAKMDGTQRRVLFDTGLVNPRGIVTDPVRGNLYWTDWNRDNPKIETSHMDGTNRRILAQDNLGLPNGLTFDAFSSQLCWVDAGTHRAECLNPAQPGRRKVLEGLQYPFAVTSYGKNLYYTDWKTNSVIAMDLAISKEMDTFHPHKQTRLYGITIALSQC 1175
                                   922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with LAMC1_MOUSE | P02468 from UniProtKB/Swiss-Prot  Length:1607

    Alignment length:164
                                   778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928    
         LAMC1_MOUSE    769 QPCPCPGGSSCAIVPKTKEVVCTHCPTGTAGKRCELCDDGYFGDPLGSNGPVRLCRPCQCNDNIDPNAVGNCNRLTGECLKCIYNTAGFYCDRCKEGFFGNPLAPNPADKCKACACNPYGTVQQQSSCNPVTGQCQCLPHVSGRDCGTCDPGYYNLQSGQGCER  932
               SCOP domains d1npeb1 B:736-792 Laminin gamma1 chain                   d1npeb2 B:793-848 Laminin gamma1 chain                  d1npeb3 B:849-899 Laminin gamma1 chain              SCOP domains
               CATH domains --1npeB01 B:738-790 Laminin                            1npeB02 B:791-846 Laminin                               1npeB03 B:847-899 Laminin                             CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------Laminin_EGF-1npeB01 B:849-897                    -- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------Laminin_EGF-1npeB02 B:849-897                    -- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------Laminin_EGF-1npeB03 B:849-897                    -- Pfam domains (3)
         Sec.struct. author ..........eee......eee......ee.....ee...eeee........eeeee............................ee.....ee...ee............ee.......hhhhh...............ee.....ee.....hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EGEGF_LAM_2  PDB: B:738-792 UniProt: 771-825             EGF_LAM_2  PDB: B:793-848 UniProt: 826-881              EGF_LAM_2  PDB: B:849-899 UniProt: 882-932          PROSITE (1)
                PROSITE (2) EGF_L----------------EGF_LAM_1  PDB: B:757-793            --------------------EGF_LAM_1  PDB: B:814-849           --------------------EGF_1       ------------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------EGF_LAM_1  PDB: B:870-899      PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1npe B  736 QPCPCPGGSSCAIVPKTKEVVCTHCPTGTAGKRCELCDDGYFGDPLGSNGPVRLCRPCQCNDNIDPNAVGNCNRLTGECLKCIYNTAGFYCDRCKEGFFGNPLAPNPADKCKACACNPYGTVQQQSSCNPVTGQCQCLPHVSGRDCGTCDPGYYNLQSGQGCER  899
                                   745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: YWTD domain (3)

Family: YWTD domain (3)

Protein domain: Nidogen (1)

Mouse (Mus musculus) [TaxId: 10090] (1)

d1npea_

Class: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: EGF/Laminin (347)

Family: Laminin-type module (3)

Protein domain: Laminin gamma1 chain (3)

Mouse (Mus musculus) [TaxId: 10090] (3)

2a	d1npeb1	B:736-792
2b	d1npeb2	B:793-848
2c	d1npeb3	B:849-899

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 6 Propellor (215)

Topology: Neuraminidase (215)

Homologous Superfamily: TolB, C-terminal domain (42)

House mouse (Mus musculus) (1)

1npeA00

A:913-1175

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

House mouse (Mus musculus) (18)

2a	1npeB01	B:738-790
2b	1npeB03	B:847-899
2c	1npeB02	B:791-846

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta_propeller (192)

Family: Ldl_recept_b (3)

Mus musculus (Mouse) (1)

1a	Ldl_recept_b-1npeA01	A:1046-1088
1b	Ldl_recept_b-1npeA02	A:1046-1088
1c	Ldl_recept_b-1npeA03	A:1046-1088

Clan: EGF (60)

Family: Laminin_EGF (4)

Mus musculus (Mouse) (4)

2a	Laminin_EGF-1npeB01	B:849-897
2b	Laminin_EGF-1npeB02	B:849-897
2c	Laminin_EGF-1npeB03	B:849-897

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NID1_MOUSE | P10493)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	GO:0050840	extracellular matrix binding	Interacting selectively and non-covalently with a component of the extracellular matrix.
	GO:0043236	laminin binding	Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells.
	GO:0043237	laminin-1 binding	Interacting selectively and non-covalently with laminin-1, a glycoprotein trimer with the subunit composition alpha1, beta1, gamma1.
	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:0043394	proteoglycan binding	Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
biological process
	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:0007160	cell-matrix adhesion	The binding of a cell to the extracellular matrix via adhesion molecules.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0032836	glomerular basement membrane development	The process whose specific outcome is the progression of the glomerular basement membrane over time, from its formation to the mature structure. The glomerular basement membrane is the basal laminal portion of the glomerulus which performs the actual filtration.
	GO:0010811	positive regulation of cell-substrate adhesion	Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
cellular component
	GO:0005605	basal lamina	A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
	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:0071944	cell periphery	The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
	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:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Chain B (LAMC1_MOUSE | P02468)

molecular function
	GO:0005201	extracellular matrix structural constituent	The action of a molecule that contributes to the structural integrity of the extracellular matrix.
	GO:0043208	glycosphingolipid binding	Interacting selectively and non-covalently with glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide.
	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:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0031581	hemidesmosome assembly	Assembly of hemidesmosomes, integrin-containing protein complexes that bind to laminin in the basal lamina. Hemidesmosomes form the contact between the basal surface of epithelial cells and the underlying basal lamina.
	GO:0031175	neuron projection development	The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0034446	substrate adhesion-dependent cell spreading	The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
cellular component
	GO:0005605	basal lamina	A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
	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: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:0043259	laminin-10 complex	A laminin complex composed of alpha5, beta1 and gamma1 polypeptide chains.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Asymmetric/Biological Unit
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		Glu A:969 - Pro A:970	[ RasMol ]

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	LAMC1_MOUSE \| P02468	:	1klo 1tle 4aqt 5mc9
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(no "Related Entries Specified in the PDB File" available for 1NPE)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (14, 14)

Cis Peptide Bonds (1, 1)

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