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PDBsum entry 1ecd

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Oxygen transport PDB id
1ecd

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
136 a.a. *
Ligands
HEM
Waters ×95
* Residue conservation analysis
PDB id:
1ecd
Name: Oxygen transport
Title: Structure of erythrocruorin in different ligand states refined at 1.4 angstroms resolution
Structure: Erythrocruorin (aquo met). Chain: a. Engineered: yes
Source: Chironomus thummi thummi. Organism_taxid: 7155. Strain: thummi
Resolution:
1.40Å     R-factor:   not given    
Authors: W.Steigemann,E.Weber
Key ref:
W.Steigemann and E.Weber (1979). Structure of erythrocruorin in different ligand states refined at 1.4 A resolution. J Mol Biol, 127, 309-338. PubMed id: 430568 DOI: 10.1016/0022-2836(79)90332-2
Date:
07-Mar-79     Release date:   05-Jul-79    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P02229  (GLB3_CHITH) -  Globin CTT-III from Chironomus thummi thummi
Seq:
Struc:
151 a.a.
136 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1016/0022-2836(79)90332-2 J Mol Biol 127:309-338 (1979)
PubMed id: 430568  
 
 
Structure of erythrocruorin in different ligand states refined at 1.4 A resolution.
W.Steigemann, E.Weber.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 7.
FIG. 7. Stereoscopic drawin of the haem group and its environment in met-erythrocruorin. The iron-ligand bonds are shown by thin lins. The bond to the water molecule is dashed, since it. is 3 A from th iron and may not really be co-ordinated to it. Polar linkages of the haem to t,hc globin and hydrogen bonds involving water molecules are represented by thin lines.
Figure 8.
FIG. 8. Difference Fourier maps with coefficients iF,(deri)/ - lF,(deoxy)l, c,(deoxy), where PJderi) are the observed structure factors of the ligation form aquomet, cerbonmonoxy, and cyaomet, respectively. The oc,(deoxy) are the calcuated phases of the refined deoxy model. Composite drawing of several sections projected parallel to the haem plane, represented by the heevy line. The vinyl-substit)uted pyrrole residues are pointing awa from the observer. The distal ide is on the left, the proximal on the right. Positive density is dran with solid lies, negative with broken lines. Contour lines beginning at 0.16 eAms with a separation of 0.08 eA-3. (a) Coefficients lE'',(aquomet) 1 - lF,(deoxy) 1, a,(deoxy). (b) Coefficients lP,(crtrbonmonoxy) 1 - IP,(deoxy) 1, cc,(deoxy). (0) Coefficients IF, (oyanomet) 1 - lF,(deoxy) /, cr,(deoxy).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1979, 127, 309-338) copyright 1979.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17693478 J.Cohen, and K.Schulten (2007).
O2 migration pathways are not conserved across proteins of a similar fold.
  Biophys J, 93, 3591-3600.  
16586113 F.A.Walker (2006).
The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography.
  J Biol Inorg Chem, 11, 391-397.  
16260762 A.Pesce, M.Nardini, S.Dewilde, D.Hoogewijs, P.Ascenzi, L.Moens, and M.Bolognesi (2005).
Modulation of oxygen binding to insect hemoglobins: the structure of hemoglobin from the botfly Gasterophilus intestinalis.
  Protein Sci, 14, 3057-3063.
PDB code: 2c0k
15917230 D.de Sanctis, S.Dewilde, C.Vonrhein, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Ponassi, M.Nardini, and M.Bolognesi (2005).
Bishistidyl heme hexacoordination, a key structural property in Drosophila melanogaster hemoglobin.
  J Biol Chem, 280, 27222-27229.
PDB code: 2bk9
12653997 S.Kamimura, A.Matsuoka, K.Imai, and K.Shikama (2003).
The swinging movement of the distal histidine residue and the autoxidation reaction for midge larval hemoglobins.
  Eur J Biochem, 270, 1424-1433.  
12211015 H.J.Park, C.Yang, N.Treff, J.D.Satterlee, and C.Kang (2002).
Crystal structures of unligated and CN-ligated Glycera dibranchiata monomer ferric hemoglobin components III and IV.
  Proteins, 49, 49-60.
PDB codes: 1jf3 1jf4 1jl6 1jl7
11167371 V.van Kampen, V.Liebers, I.Sander, Z.Chen, X.Baur, M.Raulf-Heimsoth, and F.W.Falkenberg (2001).
B-cell epitopes of the allergen Chi t 1.01: peptide mapping of epitopes recognized by rabbit, murine, and human antibodies.
  Allergy, 56, 118-125.  
10835341 A.Pesce, M.Couture, S.Dewilde, M.Guertin, K.Yamauchi, P.Ascenzi, L.Moens, and M.Bolognesi (2000).
A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family.
  EMBO J, 19, 2424-2434.
PDB codes: 1dlw 1dly
10625603 B.D.Nguyen, Z.Xia, F.Cutruzzolá, C.T.Allocatelli, M.Brunori, and G.N.La Mar (2000).
Solution (1)H NMR study of the influence of distal hydrogen bonding and N terminus acetylation on the active site electronic and molecular structure of Aplysia limacina cyanomet myoglobin.
  J Biol Chem, 275, 742-751.  
10684619 D.C.Yeh, M.V.Thorsteinsson, D.R.Bevan, M.Potts, and G.N.La Mar (2000).
Solution 1H NMR study of the heme cavity and folding topology of the abbreviated chain 118-residue globin from the cyanobacterium Nostoc commune.
  Biochemistry, 39, 1389-1399.  
10707029 J.D.Szustakowski, and Z.Weng (2000).
Protein structure alignment using a genetic algorithm.
  Proteins, 38, 428-440.  
10081963 J.A.Cuff, and G.J.Barton (1999).
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.
  Proteins, 34, 508-519.  
10037733 J.E.Knapp, M.A.Oliveira, Q.Xie, S.R.Ernst, A.F.Riggs, and M.L.Hackert (1999).
The structural and functional analysis of the hemoglobin D component from chicken.
  J Biol Chem, 274, 6411-6420.
PDB code: 1hbr
10423453 M.Bolognesi, C.Rosano, R.Losso, A.Borassi, M.Rizzi, J.B.Wittenberg, A.Boffi, and P.Ascenzi (1999).
Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study.
  Biophys J, 77, 1093-1099.
PDB codes: 1b0b 1ebc 1ebt
10542205 Z.Xia, W.Zhang, B.D.Nguyen, G.N.Mar, A.P.Kloek, and D.E.Goldberg (1999).
1H NMR investigation of the distal hydrogen bonding network and ligand tilt in the cyanomet complex of oxygen-avid Ascaris suum hemoglobin.
  J Biol Chem, 274, 31819-31826.  
9829978 S.Dewilde, M.Blaxter, M.L.Van Hauwaert, K.Van Houte, A.Pesce, N.Griffon, L.Kiger, M.C.Marden, S.Vermeire, J.Vanfleteren, E.Esmans, and L.Moens (1998).
Structural, functional, and genetic characterization of Gastrophilus hemoglobin.
  J Biol Chem, 273, 32467-32474.  
9642264 T.L.Vandergon, C.K.Riggs, T.A.Gorr, J.M.Colacino, and A.F.Riggs (1998).
The mini-hemoglobins in neural and body wall tissue of the nemertean worm, Cerebratulus lacteus.
  J Biol Chem, 273, 16998-17011.  
9578585 Y.Wu, E.Y.Chien, S.G.Sligar, and G.N.La Mar (1998).
Influence of proximal side mutations on the molecular and electronic structure of cyanomet myoglobin: an 1H NMR study.
  Biochemistry, 37, 6979-6990.  
9006947 A.K.Rashid, M.L.Van Hauwaert, M.Haque, A.H.Siddiqi, I.Lasters, M.De Maeyer, N.Griffon, M.C.Marden, S.Dewilde, J.Clauwaert, S.N.Vinogradov, and L.Moens (1997).
Trematode myoglobins, functional molecules with a distal tyrosine.
  J Biol Chem, 272, 2992-2999.  
9235002 A.L.Lomize, and H.I.Mosberg (1997).
Thermodynamic model of secondary structure for alpha-helical peptides and proteins.
  Biopolymers, 42, 239-269.  
9370468 E.E.Di Iorio, I.Tavernelli, and W.Yu (1997).
Dynamic properties of monomeric insect erythrocruorin III from Chironomus thummi-thummi: relationships between structural flexibility and functional complexity.
  Biophys J, 73, 2742-2751.  
9032082 K.S.Kroeger, and C.E.Kundrot (1997).
Structures of a hemoglobin-based blood substitute: insights into the function of allosteric proteins.
  Structure, 5, 227-237.
PDB codes: 1abw 1aby
9251819 W.Zhang, F.Cutruzzolá, C.T.Allocatelli, M.Brunori, and G.N.La Mar (1997).
A myoglobin mutant designed to mimic the oxygen-avid Ascaris suum hemoglobin: elucidation of the distal hydrogen bonding network by solution NMR.
  Biophys J, 73, 1019-1030.  
9006948 W.Zhang, K.A.Rashid, M.Haque, A.H.Siddiqi, S.N.Vinogradov, L.Moens, and G.N.Mar (1997).
Solution of 1H NMR structure of the heme cavity in the oxygen-avid myoglobin from the trematode Paramphistomum epiclitum.
  J Biol Chem, 272, 3000-3006.  
9048552 W.Zhang, K.Gersonde, and G.N.La Mar (1997).
Solution NMR study of the structural basis of the Bohr effect in the monomeric hemoglobins from Chironomus thummi thummi.
  Biochemistry, 36, 1689-1698.  
8692935 H.Hartmann, S.Zinser, P.Komninos, R.T.Schneider, G.U.Nienhaus, and F.Parak (1996).
X-ray structure determination of a metastable state of carbonmonoxy myoglobin after photodissociation.
  Proc Natl Acad Sci U S A, 93, 7013-7016.  
8816770 M.Gerstein, and C.Chothia (1996).
Packing at the protein-water interface.
  Proc Natl Acad Sci U S A, 93, 10167-10172.  
8735862 V.Liebers, I.Sander, V.Van Kampen, M.Raulf-Heimsoth, P.Rozynek, and X.Baur (1996).
Overview on denominated allergens.
  Clin Exp Allergy, 26, 494-516.  
8647133 W.Zhang, G.N.La Mar, and K.Gersonde (1996).
Solution 1H-NMR structure of the heme cavity in the low-affinity state for the allosteric monomeric cyano-met hemoglobins from Chironomus thummi thummi. Comparison to the crystal structure.
  Eur J Biochem, 237, 841-853.  
7657658 D.A.Bisig, E.E.Di Iorio, K.Diederichs, K.H.Winterhalter, and K.Piontek (1995).
Crystal structure of Asian elephant (Elephas maximus) cyano-metmyoglobin at 1.78-A resolution. Phe29(B10) accounts for its unusual ligand binding properties.
  J Biol Chem, 270, 20754-20762.
PDB code: 1emy
  8557026 U.Ermler, R.A.Siddiqui, R.Cramm, and B.Friedrich (1995).
Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution.
  EMBO J, 14, 6067-6077.
PDB code: 1cqx
7769612 W.Y.Kao, T.Hankeln, E.R.Schmidt, and G.Bergtrom (1995).
Sequence and evolution of the gene for the monomeric globin I and its linkage to genes coding for dimeric globins in the insect Chironomus thummi.
  J Mol Evol, 40, 354-361.  
7657659 X.Zhao, K.Vyas, B.D.Nguyen, K.Rajarathnam, G.N.La Mar, T.Li, G.N.Phillips, R.F.Eich, J.S.Olson, and J.Ling (1995).
A double mutant of sperm whale myoglobin mimics the structure and function of elephant myoglobin.
  J Biol Chem, 270, 20763-20774.
PDB code: 1mcy
  7756980 E.G.Hutchinson, and J.M.Thornton (1994).
A revised set of potentials for beta-turn formation in proteins.
  Protein Sci, 3, 2207-2216.  
  7849587 H.E.Aronson, W.E.Royer, and W.A.Hendrickson (1994).
Quantification of tertiary structural conservation despite primary sequence drift in the globin fold.
  Protein Sci, 3, 1706-1711.  
  7756991 M.A.Rodionov, and M.S.Johnson (1994).
Residue-residue contact substitution probabilities derived from aligned three-dimensional structures and the identification of common folds.
  Protein Sci, 3, 2366-2377.  
8198248 V.Liebers, M.Raulf, and X.Baur (1994).
Allergen-induced expression of cell surface markers on lymphocytes of Chi t I-sensitized patients.
  Allergy, 49, 163-169.  
7514489 V.Liebers, and X.Baur (1994).
Chironomidae haemoglobin Chi t I--characterization of an important inhalant allergen.
  Clin Exp Allergy, 24, 100-108.  
8456095 G.Müller, M.Gurrath, M.Kurz, and H.Kessler (1993).
Beta VI turns in peptides and proteins: a model peptide mimicry.
  Proteins, 15, 235-251.  
1515540 D.L.Weaver (1992).
Hydrophobic interaction between globin helices.
  Biopolymers, 32, 477-490.  
1518802 D.L.Weaver (1992).
Modeling microdomains: the surface area of globin helices.
  Proteins, 13, 327-335.  
  1304904 J.Overington, D.Donnelly, M.S.Johnson, A.Sali, and T.L.Blundell (1992).
Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.
  Protein Sci, 1, 216-226.  
1603814 M.J.Sippl, and S.Weitckus (1992).
Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.
  Proteins, 13, 258-271.  
1931125 A.Mattevi, G.Gatti, A.Coda, M.Rizzi, P.Ascenzi, M.Brunori, and M.Bolognesi (1991).
Binding mode of azide to ferric Aplysia limacina myoglobin. Crystallographic analysis at 1.9 A resolution.
  J Mol Recognit, 4, 1-6.
PDB code: 5mba
2065191 I.E.Iben, B.R.Cowen, R.Sanches, and J.M.Friedman (1991).
Carboxy Mb at pH 3. Time-resolved resonance Raman study at cryogenic temperatures.
  Biophys J, 59, 908-919.  
1946343 J.Kuriyan, K.Osapay, S.K.Burley, A.T.Brünger, W.A.Hendrickson, and M.Karplus (1991).
Exploration of disorder in protein structures by X-ray restrained molecular dynamics.
  Proteins, 10, 340-358.  
1957993 X.Baur, V.Liebers, G.Mazur, W.M.Becker, S.L.Kagen, and K.Kawai (1991).
Immunological cross-reactivity of hemoglobins in the Diptera family Chironomidae.
  Allergy, 46, 445-451.  
2235993 A.Pastore, and A.M.Lesk (1990).
Comparison of the structures of globins and phycocyanins: evidence for evolutionary relationship.
  Proteins, 8, 133-155.  
2235992 M.M.Teeter, X.Q.Ma, U.Rao, and M.Whitlow (1990).
Crystal structure of a protein-toxin alpha 1-purothionin at 2.5A and a comparison with predicted models.
  Proteins, 8, 118-132.  
2166604 M.Nilges, G.M.Clore, and A.M.Gronenborn (1990).
1H-NMR stereospecific assignments by conformational data-base searches.
  Biopolymers, 29, 813-822.  
2107323 M.S.Johnson, M.J.Sutcliffe, and T.L.Blundell (1990).
Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins.
  J Mol Evol, 30, 43-59.  
2622909 A.Tramontano, C.Chothia, and A.M.Lesk (1989).
Structural determinants of the conformations of medium-sized loops in proteins.
  Proteins, 6, 382-394.  
2622903 M.E.Karpen, P.L.de Haseth, and K.E.Neet (1989).
Comparing short protein substructures by a method based on backbone torsion angles.
  Proteins, 6, 155-167.  
3138426 M.Goodman, J.Pedwaydon, J.Czelusniak, T.Suzuki, T.Gotoh, L.Moens, F.Shishikura, D.Walz, and S.Vinogradov (1988).
An evolutionary tree for invertebrate globin sequences.
  J Mol Evol, 27, 236-249.  
2822413 D.H.Peyton, R.Krishnamoorthi, G.N.La Mar, K.Gersonde, K.M.Smith, and D.W.Parish (1987).
Protein-structural heterogeneity in a non-allosteric monomeric insect hemoglobin monitored by proton magnetic resonance spectroscopy.
  Eur J Biochem, 168, 377-383.  
3448607 H.Iijima, J.B.Dunbar, and G.R.Marshall (1987).
Calibration of effective van der Waals atomic contact radii for proteins and peptides.
  Proteins, 2, 330-339.  
3828462 H.M.Thompson, N.T.Yu, and K.Gersonde (1987).
Resonance Raman evidence for the mechanism of the allosteric control of O2-binding in a cobalt-substituted monomeric insect hemoglobin.
  Biophys J, 51, 289-295.  
  3709526 C.Chothia, and A.M.Lesk (1986).
The relation between the divergence of sequence and structure in proteins.
  EMBO J, 5, 823-826.  
3956482 J.D.Smit, H.Sick, A.Peterhans, and K.Gersonde (1986).
Acid Bohr effect of a monomeric haemoglobin from Dicrocoelium dendriticum. Mechanism of the allosteric conformation transition.
  Eur J Biochem, 155, 231-237.  
3709540 K.Gersonde, H.Sick, M.Overkamp, K.M.Smith, and D.W.Parish (1986).
Bohr effect in monomeric insect haemoglobins controlled by O2 off-rate and modulated by haem-rotational disorder.
  Eur J Biochem, 157, 393-404.  
3743568 N.T.Yu, H.M.Thompson, H.Mizukami, and K.Gersonde (1986).
The cobalt-nitrosyl stretching vibration as a sensitive resonance Raman probe for distal histidine-nitrosyl interaction in monomeric hemoglobins.
  Eur J Biochem, 159, 129-132.  
3720744 N.T.Yu, H.Mackin Thompson, D.Zepke, and K.Gersonde (1986).
Mechanism of the control of dioxygen binding in a dimeric cobalt-substituted insect hemoglobin. Resonance Raman evidence for cobalt-axial-ligand bond changes.
  Eur J Biochem, 157, 579-583.  
3709531 S.J.Perkins (1986).
Protein volumes and hydration effects. The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences.
  Eur J Biochem, 157, 169-180.  
3780749 V.P.Chacko, G.N.La Mar, K.Gersonde, and H.Sick (1986).
Proton-magnetic-resonance investigation of the dynamics of the conformational transition in allosteric monomeric insect hemoglobins.
  Eur J Biochem, 161, 375-381.  
6591180 N.T.Yu, B.Benko, E.A.Kerr, and K.Gersonde (1984).
Iron-carbon bond lengths in carbonmonoxy and cyanomet complexes of the monomeric hemoglobin III from Chironomus thummi thummi: a critical comparison between resonance Raman and x-ray diffraction studies.
  Proc Natl Acad Sci U S A, 81, 5106-5110.  
6422466 W.Kabsch, and C.Sander (1984).
On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.
  Proc Natl Acad Sci U S A, 81, 1075-1078.  
6617656 G.N.La Mar, R.R.Anderson, V.P.Chacko, and K.Gersonde (1983).
High-resolution proton NMR as indicator of a silent mutation in the haem cavity of a monomeric allosteric haemoglobin.
  Eur J Biochem, 136, 161-166.  
6673760 I.Glover, I.Haneef, J.Pitts, S.Wood, D.Moss, I.Tickle, and T.Blundell (1983).
Conformational flexibility in a small globular hormone: x-ray analysis of avian pancreatic polypeptide at 0.98-A resolution.
  Biopolymers, 22, 293-304.
PDB codes: 2bf9 2bgx
7097771 G.Liljeqvist, S.Paléus, and G.Braunitzer (1982).
Hemoglobins, XLVIIII. The primary structure of a monomeric hemoglobin from the hagfish, Myxine glutinosa L.: evolutionary aspects and comparative studies of the function with special reference to the heme linkage.
  J Mol Evol, 18, 102-108.  
16593093 D.H.Busch, L.L.Zimmer, J.J.Grzybowski, D.J.Olszanski, S.C.Jackels, R.C.Callahan, and G.G.Christoph (1981).
Steric control of CO binding in a totally synthetic heme protein model.
  Proc Natl Acad Sci U S A, 78, 5919-5923.  
  7216162 W.Steer, and G.Braunitzer (1981).
[Hemoglobins, XXXVI: The primary structure of a dimeric insect hemoglobin (Erythrocruorin), component IX from Chironomus thummi thummi. Studies on the quarternary structure of the dimeric CTT-hemoglobins (author's transl)]
  Hoppe Seylers Z Physiol Chem, 362, 59-71.  
  7216163 W.Steer, and G.Braunitzer (1981).
[Hemoglobins, XXXVII. The primary structure of a monomeric insect hemoglobin (Erythrocruorin), component CTT IIIa of Chironomus thummi thummi. An anomalous Heme complex: E7 Gln, E11 Ile]
  Hoppe Seylers Z Physiol Chem, 362, 73-80.  
7408841 D.Krümpelmann, W.Ribbing, and H.Rüterjans (1980).
Isomeric incorporation of the haem into monomeric haemoglobins of Chironomus thummi thummi 3. Comparative study of components, I, III and IV.
  Eur J Biochem, 108, 103-109.  
6932014 T.G.Traylor, and A.P.Berzinis (1980).
Binding of O2 and CO to hemes and hemoproteins.
  Proc Natl Acad Sci U S A, 77, 3171-3175.  
7408855 W.Ribbing, and H.Rüterjans (1980).
Isomeric incorporation of the haem into monomeric haemoglobins of Chironomus thummi thummi. 1. Isolation of chemically homogeneous haemoglobins. Evidence for the isomerism of the haem in the component III.
  Eur J Biochem, 108, 79-87.  
7408856 W.Ribbing, and H.Rüterjans (1980).
Isomeric incorporation of the Haem into monomeric haemoglobins of Chironomus thummi thummi. 2. The Bohr effect of the component III explained on a molecular basis and functional differences between the two isomeric structures.
  Eur J Biochem, 108, 89.  
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.

 

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