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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX FAB M75- PEPTIDE
 
Authors :  V. Kral, P. Mader, R. Stouracova, M. Fabry, M. Horejsi, J. Brynda
Date :  04 Jul 06  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Immunoglobulin, Fab Fragment, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Kral, P. Mader, R. Collard, M. Fabry, M. Horejsi, P. Rezacova, M. Kozisek, J. Zavada, J. Sedlacek, L. Rulisek, J. Brynda
Stabilization Of Antibody Structure Upon Association To A Human Carbonic Anhydrase Ix Epitope Studied By X-Ray Crystallography, Microcalorimetry, And Molecular Dynamics Simulations.
Proteins V. 71 1275 2008
PubMed-ID: 18041760  |  Reference-DOI: 10.1002/PROT.21821

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN LIGHT CHAIN FAB FRAGMENT
    CellHYBRIDOMA CELLS
    ChainsL
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN FAB FRAGMENT
    CellHYBRIDOMA CELLS
    ChainsH
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - CARBONIC ANHYDRASE 9
    ChainsP
    EC Number4.2.1.1
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    SynonymCARBONIC ANHYDRASE IX, CARBONATE DEHYDRATASE IX, CA-IX, CAIX, MEMBRANE ANTIGEN MN, P54/58N, RENAL CELL CARCINOMA-ASSOCIATED ANTIGEN G250, RCC-ASSOCIATED ANTIGEN G250, PMW1
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2HKF)

(-) Sites  (0, 0)

(no "Site" information available for 2HKF)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:98
2H:146 -H:201
3L:23 -L:93
4L:139 -L:199
5L:219 -H:134

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:152 -Pro H:153
5Trp H:194 -Pro H:195
6Leu P:1 -Pro P:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HKF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HKF)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003783571ENSE00001477244chr9:35673853-35674359507CAH9_HUMAN1-1351351P:1-99
1.2ENST000003783572ENSE00001091961chr9:35675535-3567556430CAH9_HUMAN135-145110--
1.3ENST000003783573ENSE00001091964chr9:35675758-35675928171CAH9_HUMAN145-202580--
1.4aENST000003783574aENSE00000928221chr9:35676061-35676203143CAH9_HUMAN202-249480--
1.5ENST000003783575ENSE00001048272chr9:35676294-3567638693CAH9_HUMAN250-280310--
1.6ENST000003783576ENSE00000928223chr9:35677787-3567785367CAH9_HUMAN281-303230--
1.7ENST000003783577ENSE00000928224chr9:35679182-35679339158CAH9_HUMAN303-355530--
1.8ENST000003783578ENSE00001048265chr9:35679851-35679995145CAH9_HUMAN356-404490--
1.9ENST000003783579ENSE00001091962chr9:35680110-3568013627CAH9_HUMAN404-413100--
1.10bENST0000037835710bENSE00000698919chr9:35680750-3568083182CAH9_HUMAN413-440280--
1.11bENST0000037835711bENSE00001835456chr9:35680962-35681156195CAH9_HUMAN440-459200--

(-) 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 H from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2hkfH01 H:1-119 Immunoglobulins                                                                                        2hkfH02 H:120-218 Immunoglobulins                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee...........eeeee........eeeee.......eeeeeeeeeee.....eeee...eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hkf H   1 EVQVVESGGGLVQPKGSLKLSCVVSGSTLNNYAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSVKDRFTISRDDSQSMIYLQMNNLKTEDTAMYYCVTYGNHPFAYWGQGTLVTVSAAKTTPPSVYPLAPGCTGSSVTLGCLVKGYFPESVTVTWNSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  143       153       168       178       188       198       208       218
                                                                                                                                                               134|                    161|                                                   
                                                                                                                                                                138                     167                                                   

Chain L from PDB  Type:PROTEIN  Length:219
 aligned with KV2A7_MOUSE | P01631 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:219
                                                                                                                                          113                                                                                                          
                                    10        20        30        40        50        60        70        80        90       100       110  |      -         -         -         -         -         -         -         -         -         -         
          KV2A7_MOUSE     1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVPPTFGGGTKLEIKR----------------------------------------------------------------------------------------------------------   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hkfL01 L:1-113 Immunoglobulins                                                                                  2hkfL02 L:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkf L   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPNLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with CAH9_HUMAN | Q16790 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:9
           CAH9_HUMAN    83 LPGEEDLPG  91
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 1 Exon 1.1  Transcript 1
                 2hkf P   1 LPGEEDLPG   9

   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  (0, 0)

(no "SCOP Domain" information available for 2HKF)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HKF)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (KV2A7_MOUSE | P01631)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain P   (CAH9_HUMAN | Q16790)
molecular function
    GO:0004089    carbonate dehydratase activity    Catalysis of the reaction: H2CO3 = CO2 + H2O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015701    bicarbonate transport    The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0002009    morphogenesis of an epithelium    The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0033574    response to testosterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
    GO:0046903    secretion    The controlled release of a substance by a cell or a tissue.
cellular component
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031528    microvillus membrane    The portion of the plasma membrane surrounding a microvillus.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAH9_HUMAN | Q167903iai 5dvx 5fl4 5fl5 5fl6
        KV2A7_MOUSE | P016311bfv 1cfv 1dlf 1maj 1mak 1n4x 1svz 1wz1 2bfv 2dlf 2hkh 2ipt 2iqa 2o5x 2o5y 2o5z 2r0w 2vq1

(-) Related Entries Specified in the PDB File

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