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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE NGB UNDER XE PRESSURE
 
Authors :  T. Moschetti, U. Mueller, J. Schultze, M. Brunori, B. Vallone
Date :  10 Mar 09  (Deposition) - 22 Sep 09  (Release) - 22 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Globin Fold, Xenon Sites, Oxygen Storage/Transport Protein Complex, Heme, Iron, Metal-Binding, Oxygen Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Moschetti, U. Mueller, J. Schultze, M. Brunori, B. Vallone
The Structure Of Neuroglobin At High Xe And Kr Pressure Reveals Partial Conservation Of Globin Internal Cavities
Biophys. J. V. 97 1700 2009
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUROGLOBIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 14B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NGB
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION
3XE4Ligand/IonXENON
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION
3XE-1Ligand/IonXENON
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO42Ligand/IonSULFATE ION
3XE-1Ligand/IonXENON

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:88 , SER A:91 , HEM A:200BINDING SITE FOR RESIDUE XE A 152
2AC2SOFTWAREALA A:29 , PHE A:32 , SER A:55 , LEU A:56 , HOH A:240BINDING SITE FOR RESIDUE XE A 153
3AC3SOFTWAREILE A:72 , HEM A:200BINDING SITE FOR RESIDUE XE A 155
4AC4SOFTWARESER A:19 , PRO A:20 , LEU A:21 , GLU A:22 , ARG A:66 , HOH A:172BINDING SITE FOR RESIDUE SO4 A 156
5AC5SOFTWARELEU A:38 , LEU A:41 , PHE A:42 , TYR A:44 , HIS A:64 , LYS A:67 , VAL A:68 , VAL A:71 , TYR A:88 , LEU A:92 , LYS A:95 , HIS A:96 , VAL A:101 , PHE A:106 , VAL A:109 , XE A:152 , XE A:155 , HOH A:163 , HOH A:194 , HOH A:215BINDING SITE FOR RESIDUE HEM A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GK9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GK9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GK9)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.NGB_MOUSE5-144  1A:5-144
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.NGB_MOUSE5-144  1A:5-144
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.NGB_MOUSE5-144  2A:5-144

(-) Exons   (0, 0)

(no "Exon" information available for 3GK9)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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   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:148
 aligned with NGB_MOUSE | Q9ER97 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
            NGB_MOUSE     3 RPESELIRQSWRVVSRSPLEHGTVLFARLFALEPSLLPLFQYNGRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLTSLGRKHRAVGVRLSSFSTVGESLLYMLEKCLGPDFTPATRTAWSRLYGAVVQAMSRGWDG 150
               SCOP domains d3gk9a_ A: Neuroglobin                                                                                                                               SCOP domains
               CATH domains 3gk9A00 A:3-150 Globins                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:5-144 UniProt: 5-144                                                                                                         ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gk9 A   3 RPESELIRQSWRVVSRSPLEHGTVLFARLFALEPSLLPLFQYNGRQFSSPEDSLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLTSLGRKHRAVGVRLSSFSTVGESLLYMLEKSLGPDFTPATRTAWSRLYGAVVQAMSRGWDG 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GK9)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (NGB_MOUSE | Q9ER97)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NGB_MOUSE | Q9ER97: 1q1f 1w92 2vry 3gkt 3gln 4mu5 4nzi 4o1t 4o2g 4o35 4o4t 4o4z 5eet 5eoh 5eqm 5eu2 5ev5 5eyj 5eys 5f0b 5f2a

(-) Related Entries Specified in the PDB File

3gkt 3gln