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(-) Description

Title :  CRYSTAL STRUCTURE OF SIDEROCALIN (NGAL, LIPOCALIN 2) COMPLEXED WITH FERRIC 4-METHYL-CATECHOL
 
Authors :  M. C. Clifton, R. K. Strong
Date :  16 Jan 09  (Deposition) - 05 May 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  8-Stranded Anti-Parallel Beta Barrel, 310-Helix, Glycoprotein, Pyrrolidone Carboxylic Acid, Secreted, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Bao, M. Clifton, T. M. Hoette, K. Mori, S. X. Deng, A. Qiu, M. Viltard, D. Williams, N. Paragas, T. Leete, R. Kulkarni, X. Li, B. Lee, A. Kalandadze, A. J. Ratner, J. C. Pizarro, K. M. Schmidt-Ott, D. W. Landry, K. N. Raymond, R. K. Strong, J. Barasch
Iron Traffics In Circulation Bound To A Siderocalin (Ngal)-Catechol Complex.
Nat. Chem. Biol. V. 6 602 2010
PubMed-ID: 20581821  |  Reference-DOI: 10.1038/NCHEMBIO.402

(-) Compounds

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T3
    Expression System StrainBL21(DE3)+RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneHNL, LCN2, NGAL
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNGAL, P25, 25 KDA ALPHA-2-MICROGLOBULIN-RELATED SUBUNIT OF MMP-9, LIPOCALIN-2, ONCOGENE 24P3

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FE3Ligand/IonFE (III) ION
3GOL9Ligand/IonGLYCEROL
4MCT3Ligand/Ion4-METHYLCATECHOL
5NA7Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
3GOL3Ligand/IonGLYCEROL
4MCT1Ligand/Ion4-METHYLCATECHOL
5NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
3GOL1Ligand/IonGLYCEROL
4MCT1Ligand/Ion4-METHYLCATECHOL
5NA-1Ligand/IonSODIUM ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
3GOL5Ligand/IonGLYCEROL
4MCT1Ligand/Ion4-METHYLCATECHOL
5NA-1Ligand/IonSODIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:106 , MCT A:180BINDING SITE FOR RESIDUE FE A 179
02AC2SOFTWARETYR A:106 , PHE A:123 , LYS A:125 , TYR A:132 , FE A:179 , HOH A:188BINDING SITE FOR RESIDUE MCT A 180
03AC3SOFTWARELYS A:30 , TYR A:32 , ASP A:177BINDING SITE FOR RESIDUE NA A 181
04AC4SOFTWARETRP A:79BINDING SITE FOR RESIDUE CL A 184
05AC5SOFTWAREASN A:114 , HIS A:118 , HOH A:375 , ASN C:116BINDING SITE FOR RESIDUE GOL A 185
06AC6SOFTWAREPRO A:162 , ASN A:164 , HIS A:165 , HOH A:348 , LYS C:75BINDING SITE FOR RESIDUE GOL A 186
07AC7SOFTWAREGLN A:117 , HOH A:347 , ASN C:114BINDING SITE FOR RESIDUE GOL A 187
08AC8SOFTWAREMCT B:180BINDING SITE FOR RESIDUE FE B 179
09AC9SOFTWARETYR B:106 , LYS B:125 , PHE B:133 , LYS B:134 , FE B:179BINDING SITE FOR RESIDUE MCT B 180
10BC1SOFTWARELEU A:13 , HOH A:235 , GLN B:88 , HOH B:246BINDING SITE FOR RESIDUE GOL B 181
11BC2SOFTWAREMCT C:180BINDING SITE FOR RESIDUE FE C 179
12BC3SOFTWARETYR C:106 , PHE C:123 , LYS C:125 , TYR C:132 , LYS C:134 , FE C:179 , GOL C:188 , HOH C:191BINDING SITE FOR RESIDUE MCT C 180
13BC4SOFTWARESER C:112 , HIS C:118BINDING SITE FOR RESIDUE NA C 181
14BC5SOFTWARELYS C:157 , HOH C:351BINDING SITE FOR RESIDUE NA C 182
15BC6SOFTWAREPHE C:22 , ASP C:24 , PRO C:85 , GLN C:88 , PRO C:89 , GLY C:90 , GLU C:91 , PHE C:92 , HOH C:205 , HOH C:240 , HOH C:242BINDING SITE FOR RESIDUE GOL C 185
16BC7SOFTWARETHR C:82 , GLY C:95 , ASN C:96 , TYR C:100BINDING SITE FOR RESIDUE GOL C 186
17BC8SOFTWARETHR C:93 , LEU C:94 , ILE C:97 , SER C:105 , TYR C:106 , HOH C:335BINDING SITE FOR RESIDUE GOL C 187
18BC9SOFTWARELYS C:125 , TYR C:132 , MCT C:180BINDING SITE FOR RESIDUE GOL C 188
19CC1SOFTWARELYS C:59 , GLU C:60 , ASP C:61BINDING SITE FOR RESIDUE GOL C 189

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:76 -A:175
2B:76 -B:175
3C:76 -C:175

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser B:5 -Asp B:6
2Lys B:73 -Lys B:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FW5)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.NGAL_HUMAN41-54
 
 
  3A:21-34
B:21-34
C:21-34
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.NGAL_HUMAN41-54
 
 
  1A:21-34
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.NGAL_HUMAN41-54
 
 
  1-
B:21-34
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.NGAL_HUMAN41-54
 
 
  1-
-
C:21-34

(-) Exons   (6, 18)

Asymmetric Unit (6, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003730171ENSE00001459333chr9:130911350-130911543194NGAL_HUMAN-00--
1.2dENST000003730172dENSE00001459332chr9:130911762-130911942181NGAL_HUMAN1-46463A:4-26
B:5-26
C:4-26
23
22
23
1.3ENST000003730173ENSE00000984625chr9:130912517-130912653137NGAL_HUMAN47-92463A:27-72
B:27-72 (gaps)
C:27-72
46
46
46
1.6bENST000003730176bENSE00000984626chr9:130913917-13091399680NGAL_HUMAN92-119283A:72-99
B:72-99
C:72-99
28
28
28
1.7ENST000003730177ENSE00000984627chr9:130914185-130914304120NGAL_HUMAN119-159413A:99-139
B:99-139
C:99-139
41
41
41
1.8ENST000003730178ENSE00001419823chr9:130914462-130914563102NGAL_HUMAN159-193353A:139-173
B:139-173 (gaps)
C:139-173
35
35
35
1.9bENST000003730179bENSE00001459311chr9:130915379-13091541234NGAL_HUMAN193-19863A:173-178
B:173-177
C:173-177
6
5
5

(-) Sequences/Alignments

Asymmetric 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:175
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:175
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     
           NGAL_HUMAN    24 TSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 198
               SCOP domains d3fw5a_ A: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh............eeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2d  PDB: A:4-26 Exon 1.3  PDB: A:27-72 UniProt: 47-92         --------------------------Exon 1.7  PDB: A:99-139 UniProt: 119-159 ---------------------------------1.9b   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.6b  PDB: A:72-99     ---------------------------------------Exon 1.8  PDB: A:139-173           ----- Transcript 1 (2)
                 3fw5 A   4 TSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173     

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:173
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   
           NGAL_HUMAN    25 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 197
               SCOP domains d3fw5b_ B: Neutrophil gelatinase-assoc      iated lipoc alin (NGAL)                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......hhhhhheeeeeeeeee....------....eeeeee.-...eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....----hhhhhhhhhh-.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------LIPOCALIN     ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2d  PDB: B:5-26Exon 1.3  PDB: B:27-72 (gaps) UniProt: 47-92  --------------------------Exon 1.7  PDB: B:99-139 UniProt: 119-159 ---------------------------------1.9b  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.6b  PDB: B:72-99     ---------------------------------------Exon 1.8  PDB: B:139-173 (gaps)    ---- Transcript 1 (2)
                 3fw5 B   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAIL------QKMYATIYELK-DKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKEL----KENFIRFSKS-GLPENHIVFPVPIDQCID 177
                                    14        24        34       | -    |   54    | | 64        74        84        94       104       114       124       134       144    |  154   | | 164       174   
                                                                42     49        59 |                                                                                144  149      158 |                 
                                                                                   61                                                                                                160                 

Chain C from PDB  Type:PROTEIN  Length:174
 aligned with NGAL_HUMAN | P80188 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:174
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    
           NGAL_HUMAN    24 TSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 197
               SCOP domains d3fw5c_ C: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh......hhhhhheeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------LIPOCALIN     ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2d  PDB: C:4-26 Exon 1.3  PDB: C:27-72 UniProt: 47-92         --------------------------Exon 1.7  PDB: C:99-139 UniProt: 119-159 ---------------------------------1.9b  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.6b  PDB: C:72-99     ---------------------------------------Exon 1.8  PDB: C:139-173           ---- Transcript 1 (2)
                 3fw5 C   4 TSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173    

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FW5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FW5)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NGAL_HUMAN | P80188)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
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:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0015891    siderophore transport    The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, 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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NGAL_HUMAN | P801881dfv 1l6m 1ngl 1qqs 1x71 1x89 1x8u 3by0 3cbc 3cmp 3dsz 3dtq 3fw4 3hwd 3hwe 3hwf 3hwg 3i0a 3k3l 3pec 3ped 3t1d 3tf6 3tzs 3u03 3u0d 4gh7 4iaw 4iax 4k19 4mvi 4mvk 4mvl 4qae 4zfx 4zhc 4zhd 4zhf 4zhg 4zhh 5jr8 5khp 5kic 5kid

(-) Related Entries Specified in the PDB File

3fw4 CRYSTAL STRUCTURE OF SIDEROCALIN (NGAL, LIPOCALIN 2) COMPLEXED WITH FERRIC CATECHOL