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(-) Description

Title :  OVOTRANSFERRIN, N-TERMINAL LOBE, HOLO FORM, AT 1.65 A RESOLUTION
 
Authors :  K. Mizutani, B. Mikami, M. Hirose
Date :  10 Apr 01  (Deposition) - 20 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferrin, Iron, Ovotransferrin, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Mizutani, B. Mikami, M. Hirose
Domain Closure Mechanism In Transferrins: New Viewpoints About The Hinge Structure And Motion As Deduced From High Resolution Crystal Structures Of Ovotransferrin N-Lobe.
J. Mol. Biol. V. 309 937 2001
PubMed-ID: 11399070  |  Reference-DOI: 10.1006/JMBI.2001.4719
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OVOTRANSFERRIN
    Chains: A
    Fragment: N-TERMINAL DOMAIN(RESIDUES 20-351)
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CO31Ligand/IonCARBONATE ION
2FE1Ligand/IonFE (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:60 , TYR A:92 , TYR A:191 , HIS A:250 , CO3 A:334BINDING SITE FOR RESIDUE FE A 333
2AC2SOFTWAREASP A:60 , TYR A:92 , THR A:117 , ARG A:121 , SER A:122 , ALA A:123 , GLY A:124 , TYR A:191 , HIS A:250 , FE A:333BINDING SITE FOR RESIDUE CO3 A 334

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:10 -A:45
2A:20 -A:36
3A:115 -A:197
4A:160 -A:174
5A:171 -A:182
6A:228 -A:242

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:70 -Pro A:71
2Gly A:286 -Pro A:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TRFE_CHICK_001 *A83VTRFE_CHICK  ---  ---AV64V
2UniProtVAR_TRFE_CHICK_002 *V100ITRFE_CHICK  ---  ---AV81I
3UniProtVAR_TRFE_CHICK_003 *R154WTRFE_CHICK  ---  ---AR135W
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSFERRIN_LIKE_4PS51408 Transferrin-like domain profile.TRFE_CHICK26-352
364-689		  1A:7-332
-
2TRANSFERRIN_LIKE_1PS00205 Transferrin-like domain signature 1.TRFE_CHICK111-120
450-459		  1A:92-101
-
3TRANSFERRIN_LIKE_2PS00206 Transferrin-like domain signature 2.TRFE_CHICK210-226
543-558		  1A:191-207
-
4TRANSFERRIN_LIKE_3PS00207 Transferrin-like domain signature 3.TRFE_CHICK242-272
584-614		  1A:223-253
-

(-) Exons   (0, 0)

(no "Exon" information available for 1IEJ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:329
 aligned with TRFE_CHICK | P02789 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:329
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
           TRFE_CHICK    23 KSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMR 351
               SCOP domains d1ieja_ A: Ovotransferrin                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1iejA01 A:5-81,A:251-316 Periplasmic binding protein-like II                 1iejA02 A:82-250,A:317-327 Periplasmic binding protein-like II                                                                                                           1iejA01 A:5-81,A:251-316 Periplasmic binding protein-like II      1iejA02    ----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhh.....eeehhhhhhhhhh.....eeeeeeeee....ee.eeeeeeeee.....hhhhh...eeee........hhhhhhhhhhh......hhhhhhhhhhhhhhh.eee......hhhhhh................hhhhhhhhhhhh....eeeee.hhhhhhh..hhh.eeee.....eee.hhh.....eeee..eeee....hhhhhhhhhhhhhhhhh................hhhhh.......eeeeee.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------V----------------I-----------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---TRANSFERRIN_LIKE_4  PDB: A:7-332 UniProt: 26-352                                                                                                                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------TRANSFERRI-----------------------------------------------------------------------------------------TRANSFERRIN_LIKE_---------------TRANSFERRIN_LIKE_3             ------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iej A   4 KSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAITLDGGQVFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMR 332
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IEJ)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRFE_CHICK | P02789)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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  1iej
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  TRFE_CHICK | P02789
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TRFE_CHICK | P02789: 1aiv 1d9k 1iq7 1jl4 1n04 1nft 1nnt 1ovt 1ryx 1tfa 2d3i

(-) Related Entries Specified in the PDB File

1nnt 1NNT CONTAINS THE SAME PROTEIN AT 2.3A RESOLUTION