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(-) Description

Title :  STRUCTURE OF THE HUMAN CSF-1:CSF-1R COMPLEX
 
Authors :  J. Felix, S. De Munck, J. Elegheert, S. N. Savvides
Date :  24 Oct 14  (Deposition) - 12 Aug 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cytokine-Cytokine Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Felix, S. De Munck, K. Verstraete, L. Meuris, N. Callewaert, J. Elegheert, S. N. Savvides
Structure And Assembly Mechanism Of The Signaling Complex Mediated By Human Csf-1.
Structure V. 23 1621 2015
PubMed-ID: 26235028  |  Reference-DOI: 10.1016/J.STR.2015.06.019

(-) Compounds

Molecule 1 - MACROPHAGE COLONY-STIMULATING FACTOR 1 RECEPTOR
    Chains: A, C
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 20-296
    Gene: CSF1R, FMS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CSF-1 RECEPTOR,M-CSF-R,PROTO-ONCOGENE C-FMS
 
Molecule 2 - MACROPHAGE COLONY-STIMULATING FACTOR 1
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 33-181
    Gene: CSF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MCSF,LANIMOSTIM

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL5Ligand/IonBETA-D-GALACTOSE
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SIA5Ligand/IonO-SIALIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGAL A:406binding site for residue SIA A 407
2AC2SOFTWAREASN A:45binding site for Mono-Saccharide NAG A 408 bound to ASN A 45
3AC3SOFTWAREASN A:73 , GLN A:77binding site for Poly-Saccharide residues NAG A 401 through SIA A 404 bound to ASN A 73
4AC4SOFTWAREASN A:153 , SIA A:407binding site for Poly-Saccharide residues NAG A 405 through GAL A 406 bound to ASN A 153
5AC5SOFTWAREASN A:275 , SER A:277 , SER A:290 , NAG C:407 , GAL C:408 , SIA C:409binding site for Poly-Saccharide residues NAG A 409 through SIA A 411 bound to ASN A 275
6AC6SOFTWAREASN C:45binding site for Mono-Saccharide NAG C 406 bound to ASN C 45
7AC7SOFTWAREASN C:73 , GLN C:77binding site for Poly-Saccharide residues NAG C 401 through SIA C 404 bound to ASN C 73
8AC8SOFTWAREASN C:153binding site for Mono-Saccharide NAG C 405 bound to ASN C 153
9AC9SOFTWAREGAL A:410 , SIA A:411 , ASN C:241 , ASN C:275 , SER C:288 , SER C:290binding site for Poly-Saccharide residues NAG C 407 through SIA C 409 bound to ASN C 275

(-) SS Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:84
2A:127 -A:177
3A:224 -A:278
4B:7 -B:90
5B:31 -D:31
6B:48 -B:139
7B:102 -B:146
8C:42 -C:84
9C:127 -C:177
10C:224 -C:278
11D:7 -D:90
12D:48 -D:139
13D:102 -D:146

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:24 -Pro A:25
2Val A:208 -Pro A:209
3Glu C:24 -Pro C:25
4Val C:208 -Pro C:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WRL)

(-) 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 A from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eeee.....eeeeee.....eee.......eeee...eeeeee...hhhhheeeeee........eeeeeeee......eee...eeeee....eee.eee.hhhhhh.eeeee.hhh.......eeee...eeee...hhhhh.eeeeeeee..eeee...eeeeee.......ee.....eeeee..eeeeeeeee....eeeeeee..ee....eeeeee..eeeeeeeeee.......eeeeeeeee...eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wrl A  20 IPVIEPSVPELVVKPGATVTLRCVGNGSVEWDGPPSPHWTLYSDGSSSILSTNNATFQNTGTYRCTEPGDPLGGSAAIHLYVKDPARPWNVLAQEVVVFEDQDALLPCLLTDPVLEAGVSLVRVRGRPLMRHTNYSFSPWHGFTIHRAKFIQSQDYQCSALMGGRKVMSISIRLKVQKVIPGPPALTLVPAELVRIRAAQIVCSASSVDVNFDVFLQHQNTKLAIPQQSDFHNNRYQKVLTLNLDVDFQHAGNYSCVASNVQGKHSTSMFFRVV 296
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      |221       231       241       251       261    || 272       282       292    
                                                                                                                                                                                                                              216|                                            266|                            
                                                                                                                                                                                                                               219                                             268                            


Chain B from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..........eeeeeehhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wrl B   2 EVSEYCSHMIGSGHLQSLQRLIDSQMETSCQITFEFVDQEQLKDPVCYLKKAFLLVQDIMEDTMRFRDNTPNAIAIVQLQELSLRLKSCFTKDYKACVRTFYETPLQLLEKVKNVFNETKNLLDKDWNIFSKNCNNSFAEC 146
                                    11        21        31        41        51        61        71        81        91   ||  105       115       125       135       145 
                                                                                                                        95|                                              
                                                                                                                        100                                              


Chain C from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eeee.....eeeeee.....eee.......eeee...eeeeee...hhhhheeeeee........eeeeeeee......eee...eeeee....eee.eee.hhhhhh.eeeee.hhh.......eeee...eeee...hhhhh.eeeeeeee..eeee...eeeeee.......ee.....eeeee....eeeeeeeee.....eeeeee..ee....eeeeee..eeeeeeeeee...hhhhheeeeeeee....eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wrl C  20 IPVIEPSVPELVVKPGATVTLRCVGNGSVEWDGPPSPHWTLYSDGSSSILSTNNATFQNTGTYRCTEPGDPLGGSAAIHLYVKDPARPWNVLAQEVVVFEDQDALLPCLLTDPVLEAGVSLVRVRGRPLMRHTNYSFSPWHGFTIHRAKFIQSQDYQCSALMGGRKVMSISIRLKVQKVIPGPPALTLVPAELVRIRGEAAQIVCSASSVDVNFDVFLQHQNTKLAIPQQSDFHNNRYQKVLTLNLDQVDFQHAGNYSCVASNVQGKHSTSMFFRVV 296
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       


Chain D from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..........eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wrl D   2 EVSEYCSHMIGSGHLQSLQRLIDSQMETSCQITFEFVDQEQLKDPVCYLKKAFLLVQDIMEDTMRFRDNTPNAIAIVQLQELSLRLKSCFTKDYKACVRTFYETPLQLLEKVKNVFNETKNLLDKDWNIFSKNCNNSFAEC 146
                                    11        21        31        41        51        61        71        81        91   ||  105       115       125       135       145 
                                                                                                                        95|                                              
                                                                                                                        100
   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 4WRL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (94, 111)

Asymmetric/Biological Unit(hide GO term definitions)

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  4wrl
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  CSF1R_HUMAN | P07333
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  CSF1_HUMAN | P09603
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  2.7.10.1
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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 4liq 4r7h 4r7i 4wrm
        CSF1_HUMAN | P09603: 1hmc 3uez 3uf2 4adf 4fa8 4wrm 5lxf

(-) Related Entries Specified in the PDB File

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