PDBsum entry 1npe

Go to PDB code: 
protein metals Protein-protein interface(s) links
Structural protein PDB id
Jmol PyMol
Protein chains
263 a.a. *
164 a.a. *
_CD ×6
Waters ×127
* Residue conservation analysis
PDB id:
Name: Structural protein
Title: Crystal structure of nidogen/laminin complex
Structure: Nidogen. Chain: a. Fragment: g3 ywtd domain, sequence database residue 941- 1203. Synonym: entactin. Engineered: yes. Laminin gamma-1 chain. Chain: b. Fragment: modules iii 3-5, sequence database residue 769-
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: nid or nid1 or ent. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: 293-ebna. Gene: lamc1.
Biol. unit: Dimer (from PQS)
2.30Å     R-factor:   0.223     R-free:   0.254
Authors: J.Takagi,Y.T.Yang,J.-H.Liu,J.-H.Wang,T.A.Springer
Key ref:
J.Takagi et al. (2003). Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface. Nature, 424, 969-974. PubMed id: 12931195 DOI: 10.1038/nature01873
17-Jan-03     Release date:   12-Aug-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P10493  (NID1_MOUSE) -  Nidogen-1
1245 a.a.
263 a.a.
Protein chain
Pfam   ArchSchema ?
P02468  (LAMC1_MOUSE) -  Laminin subunit gamma-1
1607 a.a.
164 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     basement membrane   1 term 
  Biological process     basement membrane assembly   2 terms 


DOI no: 10.1038/nature01873 Nature 424:969-974 (2003)
PubMed id: 12931195  
Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface.
J.Takagi, Y.Yang, J.H.Liu, J.H.Wang, T.A.Springer.
Basement membranes are fundamental to tissue organization and physiology in all metazoans. The interaction between laminin and nidogen is crucial to the assembly of basement membranes. The structure of the interacting domains reveals a six-bladed Tyr-Trp-Thr-Asp (YWTD) beta-propeller domain in nidogen bound to laminin epidermal-growth-factor-like (LE) modules III3-5 in laminin (LE3-5). Laminin LE module 4 binds to an amphitheatre-shaped surface on the pseudo-6-fold axis of the beta-propeller, and LE module 3 binds over its rim. A Phe residue that shutters the water-filled central aperture of the beta-propeller, the rigidity of the amphitheatre, and high shape complementarity enable the construction of an evolutionarily conserved binding surface for LE4 of unprecedentedly high affinity for its small size. Hypermorphic mutations in the Wnt co-receptor LRP5 (refs 6-9) suggest that a similar YWTD beta-propeller interface is used to bind ligands that function in developmental pathways. A related interface, but shifted off-centre from the pseudo-6-fold axis and lacking the shutter over the central aperture, is used in the low-density lipoprotein receptor for an intramolecular interaction that is regulated by pH in receptor recycling.
  Selected figure(s)  
Figure 2.
Figure 2: The nidogen beta--propeller complex with laminin modules LE3 -5 and comparison with the LDLR beta--propeller. a, Ribbon diagram of the complex. -strands are numbered on one -propeller -sheet. The two disulphide connections are black. b, Superposition of LE modules 3 (cyan), 4 (magenta), and 5 (grey). Disulphide connections are thin bonds in the same colour; Asp 800, Asn 802 and Val 804 side chains of LE4 are shown in a and b. c, Superposition of nidogen and LDLR23 -propellers showing -sheets 1 and 5. The C trace backbones, side chains and water molecules in the central channel are shown in gold (nidogen) and green (LDLR). Side chains in the hydrophobic shutter in nidogen and equivalent residues in LDLR are shown. The four water molecules present in LDLR and absent in nidogen are marked with arrows. Dashed lines in a and c represent the pseudo-6-fold axis.
Figure 4.
Figure 4: The nidogen -laminin interaction and comparison with the interaction in the LDLR. a, Stereo view of the nidogen interaction with LE4 and the adjacent portion of LE3. LE3 and LE4 are as in Fig. 2a. Portions of the nidogen backbone as C -trace and side chains forming the amphitheatre are shown in gold. Green dashed lines represent hydrogen bonds. b, C trace representation of the nidogen -laminin and intrinsic LDLR interactions. The propeller axes are vertical in the page. For clarity, the views are towards -propeller blade 1 in nidogen and blade 6 in LDLR. c, GRASP surfaces. Atoms within 4 of an interaction partner are shown in magenta (LE4 and LA4) and cyan (LE3 and LA5). The -propeller domains are viewed down their 6-fold axes. In the open book representation, the interacting LE3 -4 or LA4 -5 module pairs are rotated through 180 in the horizontal plane of the page. -propeller blades are numbered.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2003, 424, 969-974) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21481778 E.Karaca, and A.M.Bonvin (2011).
A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes.
  Structure, 19, 555-565.  
21539774 L.D.Dyksterhuis, J.F.White, M.Hickey, N.Kirby, S.Mudie, A.Hawley, A.Vashi, J.Nigro, J.A.Werkmeister, and J.A.Ramshaw (2011).
Impact of heparan sulfate chains and sulfur-mediated bonds on the mechanical properties of bovine lens capsule.
  Biophys J, 100, 2077-2083.  
19617361 C.Linke, T.T.Caradoc-Davies, P.G.Young, T.Proft, and E.N.Baker (2009).
The laminin-binding protein Lbp from Streptococcus pyogenes is a zinc receptor.
  J Bacteriol, 191, 5814-5823.
PDB code: 3gi1
19021502 D.Evseenko, K.Schenke-Layland, G.Dravid, Y.Zhu, Q.L.Hao, J.Scholes, X.C.Wang, W.R.Maclellan, and G.M.Crooks (2009).
Identification of the critical extracellular matrix proteins that promote human embryonic stem cell assembly.
  Stem Cells Dev, 18, 919-928.  
19955338 K.J.Hamill, K.Kligys, S.B.Hopkinson, and J.C.Jones (2009).
Laminin deposition in the extracellular matrix: a complex picture emerges.
  J Cell Sci, 122, 4409-4417.  
19452551 N.Kowalsman, and M.Eisenstein (2009).
Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models.
  Proteins, 77, 297-318.  
19508413 N.Saito, J.Hamada, H.Furukawa, A.Tsutsumida, A.Oyama, E.Funayama, A.Saito, T.Tsuji, M.Tada, T.Moriuchi, and Y.Yamamoto (2009).
Laminin-421 produced by lymphatic endothelial cells induces chemotaxis for human melanoma cells.
  Pigment Cell Melanoma Res, 22, 601-610.  
19355968 P.D.Yurchenco, and B.L.Patton (2009).
Developmental and pathogenic mechanisms of basement membrane assembly.
  Curr Pharm Des, 15, 1277-1294.  
19196964 T.Dainichi, S.Kurono, B.Ohyama, N.Ishii, N.Sanzen, M.Hayashi, C.Shimono, Y.Taniguchi, H.Koga, T.Karashima, S.Yasumoto, D.Zillikens, K.Sekiguchi, and T.Hashimoto (2009).
Anti-laminin gamma-1 pemphigoid.
  Proc Natl Acad Sci U S A, 106, 2800-2805.  
18359797 J.Diao, and E.Tajkhorshid (2008).
Indirect role of Ca2+ in the assembly of extracellular matrix proteins.
  Biophys J, 95, 120-127.  
18524778 L.Chen, K.Wang, Y.Shao, J.Huang, X.Li, J.Shan, D.Wu, and J.J.Zheng (2008).
Structural insight into the mechanisms of wnt signaling antagonism by dkk.
  J Biol Chem, 283, 23364-23370.
PDB code: 2jtk
19020352 M.Nagae, K.Nishikawa, N.Yasui, M.Yamasaki, T.Nogi, and J.Takagi (2008).
Structure of the F-spondin reeler domain reveals a unique beta-sandwich fold with a deformable disulfide-bonded loop.
  Acta Crystallogr D Biol Crystallogr, 64, 1138-1145.
PDB codes: 2zot 2zou
18219668 M.S.Ho, K.Böse, S.Mokkapati, R.Nischt, and N.Smyth (2008).
Nidogens-Extracellular matrix linker molecules.
  Microsc Res Tech, 71, 387-395.  
18787202 T.Nogi, T.Sangawa, S.Tabata, M.Nagae, K.Tamura-Kawakami, A.Beppu, M.Hattori, N.Yasui, and J.Takagi (2008).
Novel affinity tag system using structurally defined antibody-tag interaction: application to single-step protein purification.
  Protein Sci, 17, 2120-2126.
PDB code: 2zpk
17886339 D.Schneidman-Duhovny, R.Nussinov, and H.J.Wolfson (2007).
Automatic prediction of protein interactions with large scale motion.
  Proteins, 69, 764-773.  
17488472 J.M.Rhodes, and M.Simons (2007).
The extracellular matrix and blood vessel formation: not just a scaffold.
  J Cell Mol Med, 11, 176-205.  
17457303 M.P.Marinkovich (2007).
Tumour microenvironment: laminin 332 in squamous-cell carcinoma.
  Nat Rev Cancer, 7, 370-380.  
18044981 P.Björklund, G.Akerström, and G.Westin (2007).
An LRP5 receptor with internal deletion in hyperparathyroid tumors with implications for deregulated WNT/beta-catenin signaling.
  PLoS Med, 4, e328.  
16546374 J.J.Gray (2006).
High-resolution protein-protein docking.
  Curr Opin Struct Biol, 16, 183-193.  
16858396 T.Nogi, N.Yasui, M.Hattori, K.Iwasaki, and J.Takagi (2006).
Structure of a signaling-competent reelin fragment revealed by X-ray crystallography and electron tomography.
  EMBO J, 25, 3675-3683.
PDB code: 2ddu
15981253 C.J.Camacho (2005).
Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets.
  Proteins, 60, 245-251.  
15908573 D.Kozakov, K.H.Clodfelter, S.Vajda, and C.J.Camacho (2005).
Optimal clustering for detecting near-native conformations in protein docking.
  Biophys J, 89, 867-875.  
15981246 D.Law, M.Hotchko, and L.Ten Eyck (2005).
Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes.
  Proteins, 60, 302-307.  
15981272 D.Mustard, and D.W.Ritchie (2005).
Docking essential dynamics eigenstructures.
  Proteins, 60, 269-274.  
15981268 E.Ben-Zeev, N.Kowalsman, A.Ben-Shimon, D.Segal, T.Atarot, O.Noivirt, T.Shay, and M.Eisenstein (2005).
Docking to single-domain and multiple-domain proteins: old and new challenges.
  Proteins, 60, 195-201.  
15981245 G.Terashi, M.Takeda-Shitaka, D.Takaya, K.Komatsu, and H.Umeyama (2005).
Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues.
  Proteins, 60, 289-295.  
15952897 H.Jeon, and S.C.Blacklow (2005).
Structure and physiologic function of the low-density lipoprotein receptor.
  Annu Rev Biochem, 74, 535-562.  
15659362 J.Janin (2005).
Assessing predictions of protein-protein interaction: the CAPRI experiment.
  Protein Sci, 14, 278-283.  
15981267 J.Janin (2005).
The targets of CAPRI rounds 3-5.
  Proteins, 60, 170-175.  
15981263 K.Wiehe, B.Pierce, J.Mintseris, W.W.Tong, R.Anderson, R.Chen, and Z.Weng (2005).
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
  Proteins, 60, 207-213.  
16204884 L.J.Beamer, X.Li, C.A.Bottoms, and M.Hannink (2005).
Conserved solvent and side-chain interactions in the 1.35 Angstrom structure of the Kelch domain of Keap1.
  Acta Crystallogr D Biol Crystallogr, 61, 1335-1342.
PDB code: 1zgk
15981262 M.D.Daily, D.Masica, A.Sivasubramanian, S.Somarouthu, and J.J.Gray (2005).
CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock.
  Proteins, 60, 181-186.  
15981270 M.Zacharias (2005).
ATTRACT: protein-protein docking in CAPRI using a reduced protein model.
  Proteins, 60, 252-256.  
15824114 N.Gersdorff, E.Kohfeldt, T.Sasaki, R.Timpl, and N.Miosge (2005).
Laminin gamma3 chain binds to nidogen and is located in murine basement membranes.
  J Biol Chem, 280, 22146-22153.  
15981271 P.Carter, V.I.Lesk, S.A.Islam, and M.J.Sternberg (2005).
Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI.
  Proteins, 60, 281-288.  
15981261 R.Méndez, R.Leplae, M.F.Lensink, and S.J.Wodak (2005).
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures.
  Proteins, 60, 150-169.  
15981265 S.R.Comeau, S.Vajda, and C.J.Camacho (2005).
Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.
  Proteins, 60, 239-244.  
15981260 X.H.Ma, C.H.Li, L.Z.Shen, X.Q.Gong, W.Z.Chen, and C.X.Wang (2005).
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition.
  Proteins, 60, 319-323.  
15981251 Y.Inbar, D.Schneidman-Duhovny, I.Halperin, A.Oron, R.Nussinov, and H.J.Wolfson (2005).
Approaching the CAPRI challenge with an efficient geometry-based docking.
  Proteins, 60, 217-223.  
15296743 A.Lundell, A.I.Olin, M.Mörgelin,, A.Aspberg, and D.T.Logan (2004).
Structural basis for interactions between tenascins and lectican C-type lectin domains: evidence for a crosslinking role for tenascins.
  Structure, 12, 1495-1506.
PDB code: 1tdq
15014448 J.Culi, T.A.Springer, and R.S.Mann (2004).
Boca-dependent maturation of beta-propeller/EGF modules in low-density lipoprotein receptor proteins.
  EMBO J, 23, 1372-1380.  
15476573 M.L.Johnson, K.Harnish, R.Nusse, and W.Van Hul (2004).
LRP5 and Wnt signaling: a union made for bone.
  J Bone Miner Res, 19, 1749-1757.  
15016830 S.Hummel, A.Osanger, T.M.Bajari, M.Balasubramani, W.Halfter, J.Nimpf, and W.J.Schneider (2004).
Extracellular matrices of the avian ovarian follicle. Molecular characterization of chicken perlecan.
  J Biol Chem, 279, 23486-23494.  
15093840 S.J.Wodak, and R.Méndez (2004).
Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications.
  Curr Opin Struct Biol, 14, 242-249.  
  15215358 S.R.Comeau, D.W.Gatchell, S.Vajda, and C.J.Camacho (2004).
ClusPro: a fully automated algorithm for protein-protein docking.
  Nucleic Acids Res, 32, W96-W99.  
15037599 T.Sasaki, R.Fässler, and E.Hohenester (2004).
Laminin: the crux of basement membrane assembly.
  J Cell Biol, 164, 959-963.  
15475350 X.Li, D.Zhang, M.Hannink, and L.J.Beamer (2004).
Crystal structure of the Kelch domain of human Keap1.
  J Biol Chem, 279, 54750-54758.
PDB code: 1u6d
15143163 Y.Zhang, Y.Wang, X.Li, J.Zhang, J.Mao, Z.Li, J.Zheng, L.Li, S.Harris, and D.Wu (2004).
The LRP5 high-bone-mass G171V mutation disrupts LRP5 interaction with Mesd.
  Mol Cell Biol, 24, 4677-4684.  
14675545 G.Rudenko, and J.Deisenhofer (2003).
The low-density lipoprotein receptor: ligands, debates and lore.
  Curr Opin Struct Biol, 13, 683-689.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.