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PDBsum entry 1a22

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protein Protein-protein interface(s) links
Complex (hormone/receptor) PDB id
1a22
Jmol
Contents
Protein chains
180 a.a. *
192 a.a. *
Waters ×69
* Residue conservation analysis
PDB id:
1a22
Name: Complex (hormone/receptor)
Title: Human growth hormone bound to single receptor
Structure: Growth hormone. Chain: a. Engineered: yes. Mutation: yes. Growth hormone receptor. Chain: b. Fragment: extracellular domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.60Å     R-factor:   0.187    
Authors: A.M.De Vos,M.Ultsch
Key ref:
T.Clackson et al. (1998). Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. J Mol Biol, 277, 1111-1128. PubMed id: 9571026 DOI: 10.1006/jmbi.1998.1669
Date:
15-Jan-98     Release date:   29-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01241  (SOMA_HUMAN) -  Somatotropin
Seq:
Struc:
217 a.a.
180 a.a.*
Protein chain
Pfam   ArchSchema ?
P10912  (GHR_HUMAN) -  Growth hormone receptor
Seq:
Struc:
 
Seq:
Struc:
638 a.a.
192 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   3 terms 
  Biological process     bone maturation   16 terms 
  Biochemical function     protein binding     7 terms  

 

 
DOI no: 10.1006/jmbi.1998.1669 J Mol Biol 277:1111-1128 (1998)
PubMed id: 9571026  
 
 
Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity.
T.Clackson, M.H.Ultsch, J.A.Wells, A.M.de Vos.
 
  ABSTRACT  
 
The designed G120R mutant of human growth hormone (hGH) is an antagonist and can bind only one molecule of the growth hormone receptor. We have determined the crystal structure of the 1:1 complex between this mutant and the receptor extracellular domain (hGHbp) at 2.6 A resolution, and used it to guide a detailed survey of the structural and functional basis for hormone-receptor recognition. The overall structure of the complex is very similar to the equivalent portion of the 1:2 complex, showing that formation of the active complex does not involve major conformational changes. However, a segment involved in receptor-receptor interactions in the 1:2 complex is disordered in this structure, suggesting that its productive conformation is stabilized by receptor dimerization. The hormone binding site of the receptor comprises a central hydrophobic patch dominated by Trp104 and Trp169, surrounded by a hydrophilic periphery containing several well-ordered water molecules. Previous alanine scanning showed that the hydrophobic "hot spot" confers most of the binding energy. The new structural data, coupled with binding and kinetic analysis of further mutants, indicate that the hot spot is assembled cooperatively and that many residues contribute indirectly to binding. Several hydrophobic residues serve to orient the key tryptophan residues; kinetic analysis suggests that Pro106 locks the Trp104 main-chain into a required conformation. The electrostatic contacts of Arg43 to hGH are less important than the intramolecular packing of its alkyl chain with Trp169. The true functional epitope that directly contributes binding energy may therefore comprise as few as six side-chains, participating mostly in alkyl-aromatic stacking interactions. Outside the functional epitope, multiple mutation of residues to alanine resulted in non-additive increases in affinity: up to tenfold for a hepta-alanine mutant. Contacts in the epitope periphery can therefore attenuate the affinity of the central hot spot, perhaps reflecting a role in conferring specificity to the interaction.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo views of selected receptor-hGH interactions. In these panels, the receptor is colored green and hGH in red, water molecules are shown as red spheres, and broken lines represent hydrogen bonds. Alanine mutagenesis studies reveal that the pockets shown in (a) and (b) contain side-chains that are critical for high-affinity binding, whereas side-chain interactions shown in (c) and (d) have little effect on binding. (a) The binding pocket for Trp104. Loop EF[N] (residues 101 to 106) of the receptor interacts with residues on helix 4 (168 to 176) and 60 to 63 of hGH. A well-ordered water molecule (B=24 Å^2) bridges between the carbonyl atoms of residues Ser102 and Pro106 and the amide of Ile105. (b) The binding pocket for Trp169. Trp169 of loop BC[C] and Arg43 of loop AB[N] interact with residues 171 to 179 of helix 4 of hGH, as well as with the second minihelix (residues 64 to 68). Several water molecules are found near the periphery of the pocket (with B-factors varying between 19 and 49 Å^2). (c) Interactions between the first minihelix of hGH (residues 41 to 48) and the solvent-exposed face of the CC′FG sheet of the N-terminal domain of the receptor. (d) Interactions between residues on helix 1 of hGH and loop FG[C] of the receptor. No intermolecular hydrogen bonds are found; Glu174 of the hormone interacts with histidine residues 18 and 21.
Figure 6.
Figure 6. Residues surrounding Trp104 and Trp169 side-chains. Arg43 makes electrostatic interactions to hGH but also packs closely with Trp169. Ile103 packs against the side-chain of Trp104.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 277, 1111-1128) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB codes: 3q9n 3q9u 3qa9
20813758 L.P.Albou, O.Poch, and D.Moras (2011).
M-ORBIS: mapping of molecular binding sites and surfaces.
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Turning the growth hormone receptor on: evidence that hormone binding induces subunit rotation.
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Geometrically centered region: a "wet" model of protein binding hot spots not excluding water molecules.
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19196954 J.R.Horn, T.R.Sosnick, and A.A.Kossiakoff (2009).
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18275813 S.Li, P.Kussie, and K.M.Ferguson (2008).
Structural basis for EGF receptor inhibition by the therapeutic antibody IMC-11F8.
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PDB codes: 3b2u 3b2v
18488018 S.W.Rowlinson, H.Yoshizato, J.L.Barclay, A.J.Brooks, S.N.Behncken, L.M.Kerr, K.Millard, K.Palethorpe, K.Nielsen, J.Clyde-Smith, J.F.Hancock, and M.J.Waters (2008).
An agonist-induced conformational change in the growth hormone receptor determines the choice of signalling pathway.
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18069884 A.Del Sol, and P.Carbonell (2007).
The Modular Organization of Domain Structures: Insights into Protein-Protein Binding.
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17546660 I.S.Moreira, P.A.Fernandes, and M.J.Ramos (2007).
Hot spots--a review of the protein-protein interface determinant amino-acid residues.
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18075579 J.A.Wells, and C.L.McClendon (2007).
Reaching for high-hanging fruit in drug discovery at protein-protein interfaces.
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17441904 P.R.Hall, L.Malone, L.O.Sillerud, C.Ye, B.L.Hjelle, and R.S.Larson (2007).
Characterization and NMR solution structure of a novel cyclic pentapeptide inhibitor of pathogenic hantaviruses.
  Chem Biol Drug Des, 69, 180-190.
PDB code: 2p7r
17917757 S.Fukamachi, and A.Meyer (2007).
Evolution of receptors for growth hormone and somatolactin in fish and land vertebrates: lessons from the lungfish and sturgeon orthologues.
  J Mol Evol, 65, 359-372.  
17550252 Y.Ryabov, and D.Fushman (2007).
Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.
  J Am Chem Soc, 129, 7894-7902.
PDB codes: 2pe9 2pea
16354667 G.Song, G.A.Lazar, T.Kortemme, M.Shimaoka, J.R.Desjarlais, D.Baker, and T.A.Springer (2006).
Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion.
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16269515 J.F.Langenheim, D.Tan, A.M.Walker, and W.Y.Chen (2006).
Two wrongs can make a right: dimers of prolactin and growth hormone receptor antagonists behave as agonists.
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16948160 K.I.Cho, K.Lee, K.H.Lee, D.Kim, and D.Lee (2006).
Specificity of molecular interactions in transient protein-protein interaction interfaces.
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16511824 R.Fasan, R.L.Dias, K.Moehle, O.Zerbe, D.Obrecht, P.R.Mittl, M.G.Grütter, and J.A.Robinson (2006).
Structure-activity studies in a family of beta-hairpin protein epitope mimetic inhibitors of the p53-HDM2 protein-protein interaction.
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PDB code: 2axi
15720551 D.Hans, P.Pattnaik, A.Bhattacharyya, A.R.Shakri, S.S.Yazdani, M.Sharma, H.Choe, M.Farzan, and C.E.Chitnis (2005).
Mapping binding residues in the Plasmodium vivax domain that binds Duffy antigen during red cell invasion.
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15495260 J.Fernandez-Recio, M.Totrov, C.Skorodumov, and R.Abagyan (2005).
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16116438 R.J.Brown, J.J.Adams, R.A.Pelekanos, Y.Wan, W.J.McKinstry, K.Palethorpe, R.M.Seeber, T.A.Monks, K.A.Eidne, M.W.Parker, and M.J.Waters (2005).
Model for growth hormone receptor activation based on subunit rotation within a receptor dimer.
  Nat Struct Mol Biol, 12, 814-821.
PDB code: 2aew
15048831 M.Linhult, S.Gülich, T.Gräslund, A.Simon, M.Karlsson, A.Sjöberg, K.Nord, and S.Hober (2004).
Improving the tolerance of a protein a analogue to repeated alkaline exposures using a bypass mutagenesis approach.
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15162489 S.Liu, C.Zhang, H.Zhou, and Y.Zhou (2004).
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.
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15563602 S.T.Walsh, J.E.Sylvester, and A.A.Kossiakoff (2004).
The high- and low-affinity receptor binding sites of growth hormone are allosterically coupled.
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Molecular recognition in bone morphogenetic protein (BMP)/receptor interaction.
  Biol Chem, 385, 697-710.  
15297460 Y.Wan, A.McDevitt, B.Shen, M.L.Smythe, and M.J.Waters (2004).
Increased site 1 affinity improves biopotency of porcine growth hormone. Evidence against diffusion dependent receptor dimerization.
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Determination of the energetics governing the regulatory step in growth hormone-induced receptor homodimerization.
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14517972 G.M.Verkhivker, D.Bouzida, D.K.Gehlhaar, P.A.Rejto, S.T.Freer, and P.W.Rose (2003).
Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface.
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12842042 J.H.Chill, S.R.Quadt, R.Levy, G.Schreiber, and J.Anglister (2003).
The human type I interferon receptor: NMR structure reveals the molecular basis of ligand binding.
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PDB codes: 1n6u 1n6v
12970173 J.Takagi, K.Strokovich, T.A.Springer, and T.Walz (2003).
Structure of integrin alpha5beta1 in complex with fibronectin.
  EMBO J, 22, 4607-4615.  
12682073 K.M.Duda, and C.L.Brooks (2003).
Identification of residues outside the two binding sites that are critical for activation of the lactogenic activity of human growth hormone.
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14561755 L.A.Kuttner-Kondo, M.P.Dybvig, L.M.Mitchell, N.Muqim, J.P.Atkinson, M.E.Medof, and D.E.Hourcade (2003).
A corresponding tyrosine residue in the C2/factor B type A domain is a hot spot in the decay acceleration of the complement C3 convertases.
  J Biol Chem, 278, 52386-52391.  
12791136 M.P.Machner, S.Frese, W.D.Schubert, V.Orian-Rousseau, E.Gherardi, J.Wehland, H.H.Niemann, and D.W.Heinz (2003).
Aromatic amino acids at the surface of InlB are essential for host cell invasion by Listeria monocytogenes.
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12930995 S.T.Walsh, L.M.Jevitts, J.E.Sylvester, and A.A.Kossiakoff (2003).
Site2 binding energetics of the regulatory step of growth hormone-induced receptor homodimerization.
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12843579 Y.Kurihara, T.Watanabe, H.Nojima, M.Takeda-Shitaka, H.Sumikawa, K.Kamiya, and H.Umeyama (2003).
Dynamic character of human growth hormone and its receptor: normal mode analysis.
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12021444 A.V.Filikov, R.J.Hayes, P.Luo, D.M.Stark, C.Chan, A.Kundu, and B.I.Dahiyat (2002).
Computational stabilization of human growth hormone.
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11790828 B.Ma, M.Shatsky, H.J.Wolfson, and R.Nussinov (2002).
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations.
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12383116 D.I.Zheleva, C.McInnes, A.L.Gavine, N.Z.Zhelev, P.M.Fischer, and D.P.Lane (2002).
Highly potent p21(WAF1)-derived peptide inhibitors of CDK-mediated pRb phosphorylation: delineation and structural insight into their interactions with cyclin A.
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11839488 G.Schreiber (2002).
Kinetic studies of protein-protein interactions.
  Curr Opin Struct Biol, 12, 41-47.  
12001221 I.Halperin, B.Ma, H.Wolfson, and R.Nussinov (2002).
Principles of docking: An overview of search algorithms and a guide to scoring functions.
  Proteins, 47, 409-443.  
11790830 M.Linhult, H.K.Binz, M.Uhlén, and S.Hober (2002).
Mutational analysis of the interaction between albumin-binding domain from streptococcal protein G and human serum albumin.
  Protein Sci, 11, 206-213.  
12381794 T.Kortemme, and D.Baker (2002).
A simple physical model for binding energy hot spots in protein-protein complexes.
  Proc Natl Acad Sci U S A, 99, 14116-14121.  
11738594 K.D.Corbett, and T.Alber (2001).
The many faces of Ras: recognition of small GTP-binding proteins.
  Trends Biochem Sci, 26, 710-716.  
11479122 K.L.Morrison, and G.A.Weiss (2001).
Combinatorial alanine-scanning.
  Curr Opin Chem Biol, 5, 302-307.  
11738045 M.J.Banfield, R.L.Naylor, A.G.Robertson, S.J.Allen, D.Dawbarn, and R.L.Brady (2001).
Specificity in Trk receptor:neurotrophin interactions: the crystal structure of TrkB-d5 in complex with neurotrophin-4/5.
  Structure, 9, 1191-1199.
PDB code: 1hcf
11058219 C.E.Schutt, and U.Lindberg (2000).
Forthcoming topics
  Anat Rec, 261, 216.  
10704203 L.Runkel, C.deDios, M.Karpusas, M.Betzenhauser, C.Muldowney, M.Zafari, C.D.Benjamin, S.Miller, P.S.Hochman, and A.Whitty (2000).
Systematic mutational mapping of sites on human interferon-beta-1a that are important for receptor binding and functional activity.
  Biochemistry, 39, 2538-2551.  
10702278 R.Raffaï, K.H.Weisgraber, R.MacKenzie, B.Rupp, E.Rassart, T.Hirama, T.L.Innerarity, and R.Milne (2000).
Binding of an antibody mimetic of the human low density lipoprotein receptor to apolipoprotein E is governed through electrostatic forces. Studies using site-directed mutagenesis and molecular modeling.
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10828073 S.N.Behncken, N.Billestrup, R.Brown, J.Amstrup, B.Conway-Campbell, and M.J.Waters (2000).
Growth hormone (GH)-independent dimerization of GH receptor by a leucine zipper results in constitutive activation.
  J Biol Chem, 275, 17000-17007.  
10828942 Y.Li, H.Li, S.J.Smith-Gill, and R.A.Mariuzza (2000).
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
  Biochemistry, 39, 6296-6309.
PDB codes: 1dqj 1dqm 1dqq
  10828242 Y.Li-Smerin, and K.J.Swartz (2000).
Localization and molecular determinants of the Hanatoxin receptors on the voltage-sensing domains of a K(+) channel.
  J Gen Physiol, 115, 673-684.  
10813815 Z.Hu, B.Ma, H.Wolfson, and R.Nussinov (2000).
Conservation of polar residues as hot spots at protein interfaces.
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10075650 A.Herman, D.Helman, O.Livnah, and A.Gertler (1999).
Ruminant placental lactogens act as antagonists to homologous growth hormone receptors and as agonists to human or rabbit growth hormone receptors.
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10099129 A.Whitty, and C.W.Borysenko (1999).
Small molecule cytokine mimetics.
  Chem Biol, 6, R107-R118.  
11232291 B.M.Baker, Y.H.Ding, D.N.Garboczi, W.E.Biddison, and D.C.Wiley (1999).
Structural, biochemical, and biophysical studies of HLA-A2/altered peptide ligands binding to viral-peptide-specific human T-cell receptors.
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10413501 C.Z.Chen, and R.Shapiro (1999).
Superadditive and subadditive effects of "hot spot" mutations within the interfaces of placental ribonuclease inhibitor with angiogenin and ribonuclease A.
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10608868 H.Gårdsvoll, K.Danø, and M.Ploug (1999).
Mapping part of the functional epitope for ligand binding on the receptor for urokinase-type plasminogen activator by site-directed mutagenesis.
  J Biol Chem, 274, 37995-38003.  
  10338006 J.Pons, A.Rajpal, and J.F.Kirsch (1999).
Energetic analysis of an antigen/antibody interface: alanine scanning mutagenesis and double mutant cycles on the HyHEL-10/lysozyme interaction.
  Protein Sci, 8, 958-968.  
9974392 O.Livnah, E.A.Stura, S.A.Middleton, D.L.Johnson, L.K.Jolliffe, and I.A.Wilson (1999).
Crystallographic evidence for preformed dimers of erythropoietin receptor before ligand activation.
  Science, 283, 987-990.
PDB code: 1ern
10611645 S.N.Behncken, and M.J.Waters (1999).
Molecular recognition events involved in the activation of the growth hormone receptor by growth hormone.
  J Mol Recognit, 12, 355-362.  
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Crystallization of ovine placental lactogen in a 1:2 complex with the extracellular domain of the rat prolactin receptor.
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VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface.
  Structure, 6, 1153-1167.
PDB code: 1bj1
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.