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(-) Description

Title :  STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN CSF-1 RECEPTOR IN COMPLEX WITH THE FAB FRAGMENT OF RG7155
 
Authors :  J. Benz, I. H. Gorr, H. Hertenberger, C. H. Ries
Date :  03 Jul 13  (Deposition) - 18 Jun 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  E,H,L
Keywords :  Csf-1 Receptor, Receptor Tyrosine Kinase, Antibody, Fab Fragment, Igg Like Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. H. Ries, M. A. Cannarile, S. Hoves, J. Benz, K. Wartha, V. Runza, F. Rey-Giraud, L. P. Pradel, F. Feuerhake, I. Klaman, T. Jones, U. Jucknischke, S. Scheiblich, K. Kaluza, I. H. Gorr, A. Walz, K. Abiraj, P. A. Cassier, A. Sica, C. Gomez-Roca, K. E. De Visser, A. Italiano, C. Le Tourneau, J. P. Delord, H. Levitsky, J. Y. Blay, D. Ruttinger
Targeting Tumor-Associated Macrophages With Anti-Csf-1R Antibody Reveals A Strategy For Cancer Therapy
Cancer Cell V. 25 846 2014
PubMed-ID: 24898549  |  Reference-DOI: 10.1016/J.CCR.2014.05.016

(-) Compounds

Molecule 1 - MACROPHAGE COLONY-STIMULATING FACTOR 1 RECEPTOR
    Chains: E
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: ECTODOMAIN, UNP RESIDUES 2-512
    Gene: CSF1R
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CSF-1 RECEPTOR, CSF-1-R, CSF-1R, M-CSF-R, PROTO-ONCOGENE C- FMS
 
Molecule 2 - FAB FRAGMENT RG7155 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO-K1 SV
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HUMANIZED VERSION OF A MONOCLONAL MURINE.
 
Molecule 3 - FAB FRAGMENT RG7155 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO-K1 SV
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HUMANIZED VERSION OF A MONOCLONAL MURINE.

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : EHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH E:972 , HOH E:1015 , LYS L:39 , LYS L:42 , LYS L:45BINDING SITE FOR RESIDUE SO4 L 301
2AC2SOFTWAREASN E:240 , PHE E:270 , GLN E:271 , ALA E:273 , ASN E:275 , PHE E:292 , GLN H:3BINDING SITE FOR MONO-SACCHARIDE NAG E 807 BOUND TO ASN E 240
3AC3SOFTWAREGLY E:333 , PHE E:334 , ASN E:335 , THR E:337 , GLN E:346 , LEU E:382 , ARG E:384BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 335 RESIDUES 801 TO 804
4AC4SOFTWAREGLY E:182 , GLY E:183 , GLN E:426 , ASN E:428 , HIS E:488 , ASN E:489 , HOH E:918 , HOH E:993 , HOH E:1016BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 428 RESIDUES 805 TO 806

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1E:42 -E:84
2E:127 -E:177
3E:224 -E:278
4E:419 -E:485
5E:434 -E:441
6H:22 -H:95
7H:143 -H:199
8L:23 -L:88
9L:133 -L:193

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Glu E:24 -Pro E:25
2Ser E:55 -Pro E:56
3Val E:208 -Pro E:209
4Tyr E:328 -Pro E:329
5Tyr E:424 -Pro E:425
6Phe H:149 -Pro H:150
7Glu H:151 -Pro H:152
8Ser L:7 -Pro L:8
9Tyr L:139 -Pro L:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LIQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LIQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4LIQ)

(-) 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 E from PDB  Type:PROTEIN  Length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eeee.....eeeeee.....eee.......eeee...eeeeee...hhhhheeeeee....eeeeeee......eee...eeeee....eee.eee.hhhhhhhheeee........eeee...eeee...hhhhh.eeeeeeee..eeee...eeeeee.......eeeee..eeeee....eeeeeeeee.....eeeeee..ee....eeeee....eeeeeeeee........eeeeeeeee..eeeeeeeeeeee...eeeee.....eeeee....eeeeeeeeee....eeeeee...........eeee...eeeeeeee...hhhhheeeeeeeee..eeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee...eeeeeeee..........eeeeeee...eeee......eeeeeeee.......eeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4liq E  20 IPVIEPSVPELVVKPGATVTLRCVGNGSVEWDGPPSPHWTLYSDGSSSILSTNNATFQNTGTYRCTEPGSAAIHLYVKDPARPWNVLAQEVVVFEDQDALLPCLLTDPVLEAGVSLVRVPLMRHTNYSFSPWHGFTIHRAKFIQSQDYQCSALMGGRKVMSISIRLKVQKVIPGPPALTLVPAELVRIRGEAAQIVCSASSVDVNFDVFLQHNNTKLAIPQQSDFHNNRYQKVLTLNLDQVDFQHAGNYSCVASNVQGKHSTSMFFRVVESAYLNLSSEQNLIQEVTVGEGLNLKVMVEAYPGLQGFNWTYLGPFSDHQPEKLANATTYRHTFTLSLPRLKPSEAGRYSFLARNPGGWRALTFELTLRYPPEVSVIWTFINGSGTLLCAASGYPQPNVTWLQCSGHTDRCDEAQVLQVWDDPYPEVLSQEPFHKVTVQSLLTVETLEHNQTYECRAHNSVGSGSWAFIP 500
                                    29        39        49        59        69        79        94       104       114       124       134       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347||    |361       371       381       391       401       411       421       431       441       451       461       471       481       491         
                                                                                               88|                                              143|                                                                                                                                                                                                      348|  355|                                                                                                                                             
                                                                                                94                                               147                                                                                                                                                                                                       350   359                                                                                                                                             


Chain H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee....eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4liq H   1 QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYDISWVRQAPGQGLEWMGVIWTDGGTNYAQKLQGRVTMTTDTSTSTAYMELRSLRSDDTAVYYCARDQRLYFDVWGQGTTVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     145       155       165       175       185       195       205       215  
                                                                                                                                                            131|                                                                                
                                                                                                                                                             137                                                                                


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4liq L   1 DIQMTQSPSSLSASVGDRVTITCRASEDVNTYVSWYQQKPGKAPKLLIYAASNRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSFSYPTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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 4LIQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LIQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LIQ)

(-) Gene Ontology  (60, 60)

Asymmetric/Biological Unit(hide GO term definitions)

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  CSF1R_HUMAN | P07333
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 Related Entries

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

UniProtKB/Swiss-Prot
        CSF1R_HUMAN | P07333: 2i0v 2i0y 2i1m 2ogv 3bea 3dpk 3krj 3krl 3lcd 3lco 4dkd 4hw7 4r7h 4r7i 4wrl 4wrm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4LIQ)