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PDBsum entry 1gnc

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protein links
Growth factor PDB id
1gnc
Jmol
Contents
Protein chain
175 a.a. *
* Residue conservation analysis
PDB id:
1gnc
Name: Growth factor
Title: Structure and dynamics of the human granulocyte colony- stimulating factor determined by nmr spectroscopy. Loop mobility in a four-helix-bundle protein
Structure: Granulocyte colony-stimulating factor. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
NMR struc: 10 models
Authors: T.W.Zink,A.Ross,R.Rudolph,T.A.Holak
Key ref:
T.Zink et al. (1994). Structure and dynamics of the human granulocyte colony-stimulating factor determined by NMR spectroscopy. Loop mobility in a four-helix-bundle protein. Biochemistry, 33, 8453-8463. PubMed id: 7518249 DOI: 10.1021/bi00194a009
Date:
08-Mar-94     Release date:   31-Jul-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09919  (CSF3_HUMAN) -  Granulocyte colony-stimulating factor
Seq:
Struc:
207 a.a.
175 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     cellular response to lipopolysaccharide   17 terms 
  Biochemical function     enzyme binding     4 terms  

 

 
DOI no: 10.1021/bi00194a009 Biochemistry 33:8453-8463 (1994)
PubMed id: 7518249  
 
 
Structure and dynamics of the human granulocyte colony-stimulating factor determined by NMR spectroscopy. Loop mobility in a four-helix-bundle protein.
T.Zink, A.Ross, K.Lüers, C.Cieslar, R.Rudolph, T.A.Holak.
 
  ABSTRACT  
 
Recombinant 15N- and 13C-labeled human granulocyte colony-stimulating factor (rh-metG-CSF) has been studied by 2D and 3D NMR using uniformly labeled protein, as well as residue-specific 15N-labeled samples. Assignment of 90% of the backbone resonances and 85% of side-chain resonances has enabled the determination of both the secondary and tertiary structures of the protein. The fold is similar to those of the human growth hormone and other growth factors. Four stretches of helices were identified between residues 11 and 41 (helix A), 71 and 95 (helix B), 102 and 125 (helix C), and 145 and 170 (helix D), which form a left-handed four-helix bundle with helices A and B aligned parallel to one another (up-up) and antiparallel to helices C and D (down-down). An additional short fifth helix (E) is part of the AB loop connecting helices A and B. Examination of the protein's relaxation behavior, based on the model-free approach of Lipari and Szabo, shows that the G-CSF backbone has a well-defined structure of limited conformational flexibility in helices. In contrast, the long loop connecting helices C and D exhibits substantial fast internal motion compared to the overall rotational correlation time of the whole molecule, which is on the order of 13 ns.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
12237471 D.N.Brems (2002).
The kinetics of G-CSF folding.
  Protein Sci, 11, 2504-2511.  
11179972 C.Renner, and T.Holak (2001).
NMR 15N relaxation of the insulin-like growth factor (IGF)-binding domain of IGF binding protein-5 (IGFBP-5) determined free in solution and in complex with IGF-II.
  Eur J Biochem, 268, 1058-1065.  
  10752613 G.P.Connelly, S.G.Withers, and L.P.McIntosh (2000).
Analysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate.
  Protein Sci, 9, 512-524.  
  10794409 S.Yao, D.K.Smith, M.G.Hinds, J.G.Zhang, N.A.Nicola, and R.S.Norton (2000).
Backbone dynamics measurements on leukemia inhibitory factor, a rigid four-helical bundle cytokine.
  Protein Sci, 9, 671-682.  
10194378 C.A.McWherter, Y.Feng, L.L.Zurfluh, B.K.Klein, M.P.Baganoff, J.O.Polazzi, W.F.Hood, K.Paik, A.L.Abegg, E.S.Grabbe, J.J.Shieh, A.M.Donnelly, and J.P.McKearn (1999).
Circular permutation of the granulocyte colony-stimulating factor receptor agonist domain of myelopoietin.
  Biochemistry, 38, 4564-4571.  
10364174 J.E.Layton, G.Shimamoto, T.Osslund, A.Hammacher, D.K.Smith, H.R.Treutlein, and T.Boone (1999).
Interaction of granulocyte colony-stimulating factor (G-CSF) with its receptor. Evidence that Glu19 of G-CSF interacts with Arg288 of the receptor.
  J Biol Chem, 274, 17445-17451.  
10194377 Y.Feng, J.C.Minnerly, L.L.Zurfluh, W.D.Joy, W.F.Hood, A.L.Abegg, E.S.Grabbe, J.J.Shieh, T.L.Thurman, J.P.McKearn, and C.A.McWherter (1999).
Circular permutation of granulocyte colony-stimulating factor.
  Biochemistry, 38, 4553-4563.  
9783743 J.C.Cheetham, D.M.Smith, K.H.Aoki, J.L.Stevenson, T.J.Hoeffel, R.S.Syed, J.Egrie, and T.S.Harvey (1998).
NMR structure of human erythropoietin and a comparison with its receptor bound conformation.
  Nat Struct Biol, 5, 861-866.
PDB code: 1buy
9254611 D.H.Purvis, and B.C.Mabbutt (1997).
Solution dynamics and secondary structure of murine leukemia inhibitory factor: a four-helix cytokine with a rigid CD loop.
  Biochemistry, 36, 10146-10154.  
9187659 K.Yamasaki, S.Naito, H.Anaguchi, T.Ohkubo, and Y.Ota (1997).
Solution structure of an extracellular domain containing the WSxWS motif of the granulocyte colony-stimulating factor receptor and its interaction with ligand.
  Nat Struct Biol, 4, 498-504.
PDB codes: 1cto 1gcf
9164464 P.Fucini, C.Renner, C.Herberhold, A.A.Noegel, and T.A.Holak (1997).
The repeating segments of the F-actin cross-linking gelation factor (ABP-120) have an immunoglobulin-like fold.
  Nat Struct Biol, 4, 223-230.
PDB code: 1ksr
9230044 R.H.Folmer, M.Nilges, C.H.Papavoine, B.J.Harmsen, R.N.Konings, and C.W.Hilbers (1997).
Refined structure, DNA binding studies, and dynamics of the bacteriophage Pf3 encoded single-stranded DNA binding protein.
  Biochemistry, 36, 9120-9135.  
  9144766 R.J.Simpson, A.Hammacher, D.K.Smith, J.M.Matthews, and L.D.Ward (1997).
Interleukin-6: structure-function relationships.
  Protein Sci, 6, 929-955.  
9283089 S.J.Landry, N.K.Steede, and K.Maskos (1997).
Temperature dependence of backbone dynamics in loops of human mitochondrial heat shock protein 10.
  Biochemistry, 36, 10975-10986.  
9249051 V.Gervais, A.Zerial, and H.Oschkinat (1997).
NMR investigations of the role of the sugar moiety in glycosylated recombinant human granulocyte-colony-stimulating factor.
  Eur J Biochem, 247, 386-395.  
  8745404 H.S.Cho, C.W.Liu, F.F.Damberger, J.G.Pelton, H.C.Nelson, and D.E.Wemmer (1996).
Yeast heat shock transcription factor N-terminal activation domains are unstructured as probed by heteronuclear NMR spectroscopy.
  Protein Sci, 5, 262-269.  
8755711 J.Habazettl, L.C.Myers, F.Yuan, G.L.Verdine, and G.Wagner (1996).
Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR.
  Biochemistry, 35, 9335-9348.  
8664278 J.P.MacKay, G.L.Shaw, and G.F.King (1996).
Backbone dynamics of the c-Jun leucine zipper: 15N NMR relaxation studies.
  Biochemistry, 35, 4867-4877.  
8930100 K.T.Dayie, G.Wagner, and J.F.Lefèvre (1996).
Theory and practice of nuclear spin relaxation in proteins.
  Annu Rev Phys Chem, 47, 243-282.  
8703937 L.Yu, C.X.Zhu, Y.C.Tse-Dinh, and S.W.Fesik (1996).
Backbone dynamics of the C-terminal domain of Escherichia coli topoisomerase I in the absence and presence of single-stranded DNA.
  Biochemistry, 35, 9661-9666.  
  8897610 P.Mühlhahn, J.Bernhagen, M.Czisch, J.Georgescu, C.Renner, A.Ross, R.Bucala, and T.A.Holak (1996).
NMR characterization of structure, backbone dynamics, and glutathione binding of the human macrophage migration inhibitory factor (MIF).
  Protein Sci, 5, 2095-2103.  
8784206 V.De Filippis, P.P.de Laureto, N.Toniutti, and A.Fontana (1996).
Acid-induced molten globule state of a fully active mutant of human interleukin-6.
  Biochemistry, 35, 11503-11511.  
7773741 H.R.Mott, and I.D.Campbell (1995).
Four-helix bundle growth factors and their receptors: protein-protein interactions.
  Curr Opin Struct Biol, 5, 114-121.  
  7663341 R.T.Clubb, J.G.Omichinski, K.Sakaguchi, E.Appella, A.M.Gronenborn, and G.M.Clore (1995).
Backbone dynamics of the oligomerization domain of p53 determined from 15N NMR relaxation measurements.
  Protein Sci, 4, 855-862.  
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.