PDBsum entry 1ucs

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protein links
Antifreeze protein PDB id
Jmol PyMol
Protein chain
64 a.a. *
Waters ×240
* Residue conservation analysis
PDB id:
Name: Antifreeze protein
Title: Type iii antifreeze protein rd1 from an antarctic eel pout
Structure: Antifreeze peptide rd1. Chain: a. Synonym: type iii antifreeze protein rd1
Source: Lycodichthys dearborni. Antarctic eel pout. Organism_taxid: 8201
0.62Å     R-factor:   0.139     R-free:   0.155
Authors: T.-P.Ko,H.Robinson,Y.-G.Gao,C.-H.C.Cheng,A.L.Devries,A.H.- J.Wang
Key ref: T.P.Ko et al. (2003). The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation. Biophys J, 84, 1228-1237. PubMed id: 12547803
21-Apr-03     Release date:   06-May-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P35751  (ANP1_RHIDE) -  Ice-structuring protein RD1
64 a.a.
64 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 


Biophys J 84:1228-1237 (2003)
PubMed id: 12547803  
The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation.
T.P.Ko, H.Robinson, Y.G.Gao, C.H.Cheng, A.L.DeVries, A.H.Wang.
RD1 is a 7-kDa globular protein from the Antarctic eel pout Lycodichthys dearborni. It belongs to type III of the four types of antifreeze proteins (AFPs) found in marine fishes living at subzero temperatures. For type III AFP, a potential ice-binding flat surface has been identified and is imbedded with side chains capable of making hydrogen bonds with a specific lattice plane on ice. So far, all crystallographic studies on type III AFPs were carried out using the Atlantic ocean pout Macrozoarces americanus as the source organism. Here we present the crystal structure of a type III AFP from a different zoarcid fish, and at an ultra-high resolution of 0.62 A. The protein fold of RD1 comprises a compact globular domain with two internal tandem motifs arranged about a pseudo-dyad symmetry. Each motif of the "pretzel fold" includes four short beta-strands and a 3(10) helix. There is a novel internal cavity of 45 A(3) surrounded by eight conserved nonpolar residues. The model contains several residues with alternate conformations, and a number of split water molecules, probably caused by alternate interactions with the protein molecule. After extensive refinement that includes hydrogen atoms, significant residual electron densities associated with the electrons of peptides and many other bonds could be visualized.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21482800 C.P.Garnham, R.L.Campbell, and P.L.Davies (2011).
Anchored clathrate waters bind antifreeze proteins to ice.
  Proc Natl Acad Sci U S A, 108, 7363-7367.
PDB code: 3p4g
21472814 E.I.Howard, M.P.Blakeley, M.Haertlein, I.P.Haertlein, A.Mitschler, S.J.Fisher, A.C.Siah, A.G.Salvay, A.Popov, C.M.Dieckmann, T.Petrova, and A.Podjarny (2011).
Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface.
  J Mol Recognit, 24, 724-732.
PDB code: 3qf6
20371498 D.Zhi, M.Shatsky, and S.E.Brenner (2010).
Alignment-free local structural search by writhe decomposition.
  Bioinformatics, 26, 1176-1184.  
20737588 H.L.Chen, J.C.Hsu, M.H.Viet, M.S.Li, C.K.Hu, C.H.Liu, F.Y.Luh, S.S.Chen, E.S.Chang, A.H.Wang, M.F.Hsu, W.Fann, and R.P.Chen (2010).
Studying submicrosecond protein folding kinetics using a photolabile caging strategy and time-resolved photoacoustic calorimetry.
  Proteins, 78, 2973-2983.  
20686757 J.L.Kelley, J.E.Aagaard, M.J.MacCoss, and W.J.Swanson (2010).
Functional diversification and evolution of antifreeze proteins in the antarctic fish Lycodichthys dearborni.
  J Mol Evol, 71, 111-118.  
19383454 D.L.Masica, and J.J.Gray (2009).
Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system.
  Biophys J, 96, 3082-3091.  
  19342793 I.Petit-Haertlein, M.P.Blakeley, E.Howard, I.Hazemann, A.Mitschler, M.Haertlein, and A.Podjarny (2009).
Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 406-409.  
18814299 P.Labute (2009).
Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures.
  Proteins, 75, 187-205.  
18453693 B.Guillot, C.Jelsch, A.Podjarny, and C.Lecomte (2008).
Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.
  Acta Crystallogr D Biol Crystallogr, 64, 567-588.  
18421138 C.Lecomte, C.Jelsch, B.Guillot, B.Fournier, and A.Lagoutte (2008).
Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteins.
  J Synchrotron Radiat, 15, 202-203.  
18323618 E.Nishibori, T.Nakamura, M.Arimoto, S.Aoyagi, H.Ago, M.Miyano, T.Ebisuzaki, and M.Sakata (2008).
Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3 A X-ray diffraction data.
  Acta Crystallogr D Biol Crystallogr, 64, 237-247.  
17242509 A.Volkov, M.Messerschmidt, and P.Coppens (2007).
Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures.
  Acta Crystallogr D Biol Crystallogr, 63, 160-170.  
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
18084073 J.Wang, M.Dauter, R.Alkire, A.Joachimiak, and Z.Dauter (2007).
Triclinic lysozyme at 0.65 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 1254-1268.
PDB code: 2vb1
17452786 M.Jaskolski, M.Gilski, Z.Dauter, and A.Wlodawer (2007).
Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?
  Acta Crystallogr D Biol Crystallogr, 63, 611-620.  
17189482 O.García-Arribas, R.Mateo, M.M.Tomczak, P.L.Davies, and M.G.Mateu (2007).
Thermodynamic stability of a cold-adapted protein, type III antifreeze protein, and energetic contribution of salt bridges.
  Protein Sci, 16, 227-238.  
18007035 P.V.Afonine, R.W.Grosse-Kunstleve, P.D.Adams, V.Y.Lunin, and A.Urzhumtsev (2007).
On macromolecular refinement at subatomic resolution with interatomic scatterers.
  Acta Crystallogr D Biol Crystallogr, 63, 1194-1197.  
16707576 A.K.Katz, X.Li, H.L.Carrell, B.L.Hanson, P.Langan, L.Coates, B.P.Schoenborn, J.P.Glusker, and G.J.Bunick (2006).
Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction.
  Proc Natl Acad Sci U S A, 103, 8342-8347.
PDB codes: 2glk 2gub 2gve
16552136 J.Hakanpää, M.Linder, A.Popov, A.Schmidt, and J.Rouvinen (2006).
Hydrophobin HFBII in detail: ultrahigh-resolution structure at 0.75 A.
  Acta Crystallogr D Biol Crystallogr, 62, 356-367.
PDB code: 2b97
19079786 N.Yu, S.A.Hayik, B.Wang, N.Liao, C.H.Reynolds, and K.M.Merz (2006).
Assigning the protonation states of the key aspartates in beta-Secretase using QM/MM X-ray structure refinement.
  J Chem Theory Comput, 2, 1057-1069.  
17132861 N.Yu, X.Li, G.Cui, S.A.Hayik, and K.M.Merz (2006).
Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement.
  Protein Sci, 15, 2773-2784.  
16597820 T.Hamada, Y.Ito, T.Abe, F.Hayashi, P.Güntert, M.Inoue, T.Kigawa, T.Terada, M.Shirouzu, M.Yoshida, A.Tanaka, S.Sugano, S.Yokoyama, and H.Hirota (2006).
Solution structure of the antifreeze-like domain of human sialic acid synthase.
  Protein Sci, 15, 1010-1016.
PDB code: 1wvo
  16754975 Y.Nishimiya, H.Kondo, M.Yasui, H.Sugimoto, N.Noro, R.Sato, M.Suzuki, A.Miura, and S.Tsuda (2006).
Crystallization and preliminary X-ray crystallographic analysis of Ca2+-independent and Ca2+-dependent species of the type II antifreeze protein.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 538-541.  
15983423 H.Bönisch, C.L.Schmidt, P.Bianco, and R.Ladenstein (2005).
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.
  Acta Crystallogr D Biol Crystallogr, 61, 990.
PDB codes: 1yk4 1yk5
15654886 Y.Nishimiya, R.Sato, M.Takamichi, A.Miura, and S.Tsuda (2005).
Co-operative effect of the isoforms of type III antifreeze protein expressed in Notched-fin eelpout, Zoarces elongatus Kner.
  FEBS J, 272, 482-492.  
15333922 A.K.Pedersen, G.H.Peters G, K.B.Møller, L.F.Iversen, and J.S.Kastrup (2004).
Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B.
  Acta Crystallogr D Biol Crystallogr, 60, 1527-1534.
PDB code: 1sug
14747702 P.V.Afonine, V.Y.Lunin, N.Muzet, and A.Urzhumtsev (2004).
On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps.
  Acta Crystallogr D Biol Crystallogr, 60, 260-274.  
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.