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PDBsum entry 1i1j

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protein links
Hormone/growth factor PDB id
1i1j
Jmol
Contents
Protein chain
106 a.a. *
Waters ×212
* Residue conservation analysis
PDB id:
1i1j
Name: Hormone/growth factor
Title: Structure of melanoma inhibitory activity protein: a member of a new family of secreted proteins
Structure: Melanoma derived growth regulatory protein. Chain: a, b. Synonym: melanoma inhibitory activity. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.39Å     R-factor:   0.209     R-free:   0.231
Authors: J.C.Lougheed,J.M.Holton,T.Alber,J.F.Bazan,T.M.Handel
Key ref:
J.C.Lougheed et al. (2001). Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins. Proc Natl Acad Sci U S A, 98, 5515-5520. PubMed id: 11331761 DOI: 10.1073/pnas.091601698
Date:
02-Feb-01     Release date:   16-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q16674  (MIA_HUMAN) -  Melanoma-derived growth regulatory protein
Seq:
Struc:
131 a.a.
106 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     cell proliferation   1 term 
  Biochemical function     growth factor activity     1 term  

 

 
DOI no: 10.1073/pnas.091601698 Proc Natl Acad Sci U S A 98:5515-5520 (2001)
PubMed id: 11331761  
 
 
Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins.
J.C.Lougheed, J.M.Holton, T.Alber, J.F.Bazan, T.M.Handel.
 
  ABSTRACT  
 
Melanoma inhibitory activity (MIA) is a 12-kDa protein that is secreted from both chondrocytes and malignant melanoma cells. MIA has been reported to have effects on cell growth and adhesion, and it may play a role in melanoma metastasis and cartilage development. We report the 1.4-A crystal structure of human MIA, which consists of an Src homology 3 (SH3)-like domain with N- and C-terminal extensions of about 20 aa. each. The N- and C-terminal extensions add additional structural elements to the SH3 domain, forming a previously undescribed fold. MIA is a representative of a recently identified family of proteins and is the first structure of a secreted protein with an SH3 subdomain. The structure also suggests a likely protein interaction site and suggests that, unlike conventional SH3 domains, MIA does not recognize polyproline helices.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The structure of melanoma inhibitory activity protein. -strands are in blue, regions lacking regular secondary structure are in green, 3[10] helices are in red, and disulfide bonds are in gold. (A) View of the two sheets that pack at right angles to each other. Sheet I is in front. 1 and 7 add onto sheet II of the SH3 -sandwich. The top of the barrel is toward the top of the page. (B) View looking into one end (mouth) of the barrel. The 30s-40s loop (analogous to the RT loop of SH3 domains) and the 60s-70s loop, flank one mouth of the barrel. The N-terminal residues preceding 1 and the C-terminal residues following 7 run along the outside face of sheet II. A and B are on the same scale.
Figure 4.
Fig. 4. Comparison of the SH3 polyproline helix binding site to the analogous region in MIA. (A) Superposition of the conserved residues in the polyproline helix binding site of Sem-5 (red) and the corresponding residues in MIA (blue). Four of six residues conserved in SH3 domains differ in MIA. Residue numbering corresponds to MIA. Residues listed in parentheses are those found in canonical SH3 domains. (B) View of the molecular surfaces of MIA (Left) and the Sem-5 SH3 domain (Right). The structure of Sem-5 is shown with its polyproline ligand bound. Sem-5 residues colored in red are those that make up a triad of conserved aromatic residues arranged approximately linearly on the molecular surface. The dissimilarity of the corresponding residues in MIA, F59, I83, and Q28 result in a much smoother molecular surface that most likely does not recognize polyproline helices.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19942856 F.Wendler, A.K.Gillingham, R.Sinka, C.Rosa-Ferreira, D.E.Gordon, X.Franch-Marro, A.A.Peden, J.P.Vincent, and S.Munro (2010).
A genome-wide RNA interference screen identifies two novel components of the metazoan secretory pathway.
  EMBO J, 29, 304-314.  
20164682 T.Schubert, J.Schlegel, R.Schmid, A.Opolka, S.Grassel, M.Humphries, and A.K.Bosserhoff (2010).
Modulation of cartilage differentiation by melanoma inhibiting activity/cartilage-derived retinoic acid-sensitive protein (MIA/CD-RAP).
  Exp Mol Med, 42, 166-174.  
19521988 J.Schmidt, and A.K.Bosserhoff (2009).
Processing of MIA protein during melanoma cell migration.
  Int J Cancer, 125, 1587-1594.  
19111067 R.R.Thangudu, M.Manoharan, N.Srinivasan, F.Cadet, R.Sowdhamini, and B.Offmann (2008).
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families.
  BMC Struct Biol, 8, 55.  
18342301 S.Lin, M.Ikegami, Y.Xu, A.K.Bosserhoff, A.M.Malkinson, and J.M.Shannon (2008).
Misexpression of MIA disrupts lung morphogenesis and causes neonatal death.
  Dev Biol, 316, 441-455.  
18513436 S.Sandhya, B.Pankaj, M.K.Govind, B.Offmann, N.Srinivasan, and R.Sowdhamini (2008).
CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations.
  BMC Struct Biol, 8, 28.  
16369097 A.A.Lebedev, A.A.Vagin, and G.N.Murshudov (2006).
Intensity statistics in twinned crystals with examples from the PDB.
  Acta Crystallogr D Biol Crystallogr, 62, 83-95.  
16467855 J.R.Mesters, C.Barinka, W.Li, T.Tsukamoto, P.Majer, B.S.Slusher, J.Konvalinka, and R.Hilgenfeld (2006).
Structure of glutamate carboxypeptidase II, a drug target in neuronal damage and prostate cancer.
  EMBO J, 25, 1375-1384.
PDB codes: 2c6c 2c6g 2c6p
17132106 R.Stoll, S.Lodermeyer, and A.K.Bosserhoff (2006).
Detailed analysis of MIA protein by mutagenesis.
  Biol Chem, 387, 1601-1606.  
17044017 S.Arndt, and A.K.Bosserhoff (2006).
TANGO is a tumor suppressor of malignant melanoma.
  Int J Cancer, 119, 2812-2820.  
15760338 J.Tatzel, I.Poser, J.Schroeder, and A.K.Bosserhoff (2005).
Inhibition of melanoma inhibitory activity (MIA) expression in melanoma cells leads to molecular and phenotypic changes.
  Pigment Cell Res, 18, 92.  
14752198 J.Holton, and T.Alber (2004).
Automated protein crystal structure determination using ELVES.
  Proc Natl Acad Sci U S A, 101, 1537-1542.
PDB codes: 1rb1 1rb4 1rb5 1rb6 3k7z
15298926 W.Li, Y.Zhang, and J.Skolnick (2004).
Application of sparse NMR restraints to large-scale protein structure prediction.
  Biophys J, 87, 1241-1248.  
12592021 R.Stoll, C.Renner, R.Buettner, W.Voelter, A.K.Bosserhoff, and T.A.Holak (2003).
Backbone dynamics of the human MIA protein studied by (15)N NMR relaxation: implications for extended interactions of SH3 domains.
  Protein Sci, 12, 510-519.  
14517980 W.Li, Y.Zhang, D.Kihara, Y.J.Huang, D.Zheng, G.T.Montelione, A.Kolinski, and J.Skolnick (2003).
TOUCHSTONEX: protein structure prediction with sparse NMR data.
  Proteins, 53, 290-306.  
12140381 K.Wakamatsu, T.Kageshita, M.Furue, N.Hatta, Y.Kiyohara, J.Nakayama, T.Ono, T.Saida, M.Takata, T.Tsuchida, H.Uhara, A.Yamamoto, N.Yamazaki, A.Naito, and S.Ito (2002).
Evaluation of 5-S-cysteinyldopa as a marker of melanoma progression: 10 years' experience.
  Melanoma Res, 12, 245-253.  
11839810 M.Moser, A.K.Bosserhoff, E.B.Hunziker, L.Sandell, R.Fässler, and R.Buettner (2002).
Ultrastructural cartilage abnormalities in MIA/CD-RAP-deficient mice.
  Mol Cell Biol, 22, 1438-1445.  
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 codes are shown on the right.