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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THIRD FIBRONECTIN DOMAIN (FN3) OF HUMAN ROBO1 IN COMPLEX WITH THE FAB FRAGMENT OF MURINE MONOCLONAL ANTIBODY B2212A.
 
Authors :  T. Nakayama, E. Mizohata, T. Yamashita, M. Nagatoishi, H. Iwanari, Y. M Y. Kado, Y. Yokota, R. Sato, K. Tsumoto, H. Fujitani, T. Kodama, T. Hama T. Inoue
Date :  12 Sep 13  (Deposition) - 21 Jan 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,H,I,L,M
Biol. Unit 1:  A,H,L  (1x)
Biol. Unit 2:  B,I,M  (1x)
Keywords :  Fibronectin Type-Iii Domain, Hepatocellular Carcinoma Antigen, Angiogenesis, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nakayama, E. Mizohata, T. Yamashita, S. Nagatoishi, M. Nakakido, H. Iwanari, Y. Mochizuki, Y. Kado, Y. Yokota, R. Satoh, K. Tsumoto, H. Fujitani, T. Kodama, T. Hamakubo, T. Inoue
Structural Features Of Interfacial Tyrosine Residue In Robo Fibronectin Domain-Antibody Complex: Crystallographic, Thermodynamic, And Molecular Dynamic Analyses
Protein Sci. V. 24 328 2015
PubMed-ID: 25492858  |  Reference-DOI: 10.1002/PRO.2619

(-) Compounds

Molecule 1 - ROUNDABOUT HOMOLOG 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDUTT1, ROBO1, ROUNDABOUT HOMOLOG 1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDELETED IN U TWENTY TWENTY, H-ROBO-1
 
Molecule 2 - ANTI-HUMAN ROBO1 ANTIBODY B2212A FAB LIGHT CHAIN
    ChainsL, M
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - ANTI-HUMAN ROBO1 ANTIBODY B2212A FAB HEAVY CHAIN
    ChainsH, I
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABHILM
Biological Unit 1 (1x)A H L 
Biological Unit 2 (1x) B I M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN H:111 , GLY H:112 , THR H:114 , HOH H:462BINDING SITE FOR RESIDUE GOL H 301
2AC2SOFTWAREVAL I:93 , TYR I:95 , GLN I:111 , GLY I:112 , THR I:114 , HOH I:1178 , HOH I:1385 , GLY M:42BINDING SITE FOR RESIDUE GOL I 1001

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:146 -H:201
3I:22 -I:96
4I:146 -I:201
5L:23 -L:88
6L:134 -L:194
7M:23 -M:88
8M:134 -M:194

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Leu L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Phe H:152 -Pro H:153
4Glu H:154 -Pro H:155
5Trp H:194 -Pro H:195
6Asp B:15 -Gly B:16
7Leu M:94 -Pro M:95
8Tyr M:140 -Pro M:141
9Phe I:152 -Pro I:153
10Glu I:154 -Pro I:155
11Trp I:194 -Pro I:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WIH)

(-) Exons   (0, 0)

(no "Exon" information available for 3WIH)

(-) 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:88
 aligned with ROBO1_HUMAN | Q9Y6N7 from UniProtKB/Swiss-Prot  Length:1651

    Alignment length:96
                                   786       796       806       816       826       836       846       856       866      
          ROBO1_HUMAN   777 APPQGVTVSKNDGNGTAILVSWQPPPEDTQNGMVQEYKVWCLGNETRYHINKTVDGSTFSVVIPFLVPGIRYSVEVAASTGAGSGVKSEPQFIQLD 872
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.......eeeeee....-----...eeeeeee..hhhhheeeeee....eeee........eeeeeee.---........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3wih A   4 APPQGVTVSKNDGNGTAILVSWQPPPE-----MVQEYKVWCLGNETRYHINKTVDGSTFSVVIPFLVPGIRYSVEVAAS---GSGVKSEPQFIQLD  99
                                    13        23      |  -  |     43        53        63        73        |-  |     93      
                                                     30    36                                            82  86             

Chain B from PDB  Type:PROTEIN  Length:88
 aligned with ROBO1_HUMAN | Q9Y6N7 from UniProtKB/Swiss-Prot  Length:1651

    Alignment length:96
                                   786       796       806       816       826       836       846       856       866      
          ROBO1_HUMAN   777 APPQGVTVSKNDGNGTAILVSWQPPPEDTQNGMVQEYKVWCLGNETRYHINKTVDGSTFSVVIPFLVPGIRYSVEVAASTGAGSGVKSEPQFIQLD 872
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.......eeeeee....-----...eeeeeee..hhhhheeeeee....eeee........eeeeeee.---........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3wih B   4 APPQGVTVSKNDGNGTAILVSWQPPPE-----MVQEYKVWCLGNETRYHINKTVDGSTFSVVIPFLVPGIRYSVEVAAS---GSGVKSEPQFIQLD  99
                                    13        23      |  -  |     43        53        63        73        |-  |     93      
                                                     30    36                                            82  86             

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wih H   1 EVQLQQSGPELVKPGASVKISCKASGYTFTDYYMNWVKLSHGKSLEWIGDIVPNNGDTTYNQNFRGKATLTVDKSSSTAYMELRSLTSEDSAVYYCARFSNYVYPFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAILQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         

Chain I from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wih I   1 EVQLQQSGPELVKPGASVKISCKASGYTFTDYYMNWVKLSHGKSLEWIGDIVPNNGDTTYNQNFRGKATLTVDKSSSTAYMELRSLTSEDSAVYYCARFSNYVYPFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAILQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wih L   1 DIQMTQTTSSLSASLGDRVTISCRASQDISNFLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDFSLTISKLEQEDIATYFCQQGNTLPLTFGAGTKLELKRAEAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wih M   1 DIQMTQTTSSLSASLGDRVTISCRASQDISNFLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDFSLTISKLEQEDIATYFCQQGNTLPLTFGAGTKLELKRAEAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

   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 3WIH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ROBO1_HUMAN | Q9Y6N7)
molecular function
    GO:0030275    LRR domain binding    Interacting selectively and non-covalently with a LRR domain (leucine rich repeats) of a protein.
    GO:0008046    axon guidance receptor activity    Combining with an extracellular messenger and transmitting the signal from one side of the membrane to the other to results in a change in cellular activity involved in axon guidance.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0035385    Roundabout signaling pathway    A series of molecular signals initiated by the binding of a SLIT protein to a Roundabout (ROBO) family receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0016199    axon midline choice point recognition    The recognition of molecules at the central nervous system midline choice point by an axon growth cone; this choice point determines whether the growth cone will cross the midline.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0002042    cell migration involved in sprouting angiogenesis    The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis.
    GO:0021836    chemorepulsion involved in postnatal olfactory bulb interneuron migration    The creation and reception of signals that repel olfactory bulb interneurons from the subventricular zone as a component process in tangential migration.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007156    homophilic cell adhesion via plasma membrane adhesion molecules    The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0070100    negative regulation of chemokine-mediated signaling pathway    Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of a chemokine binding to a cell surface receptor.
    GO:0033600    negative regulation of mammary gland epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of mammary gland epithelial cell proliferation.
    GO:0050925    negative regulation of negative chemotaxis    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism towards a lower concentration in a concentration gradient of a specific chemical.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0035025    positive regulation of Rho protein signal transduction    Any process that activates or increases the frequency, rate or extent of Rho protein signal transduction.
    GO:0050772    positive regulation of axonogenesis    Any process that activates or increases the frequency, rate or extent of axonogenesis.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005887    integral component of plasma membrane    The component of the plasma 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: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)

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        ROBO1_HUMAN | Q9Y6N72eo9 2v9q 2v9r 2v9t 4hlj

(-) Related Entries Specified in the PDB File

3wii