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(-) Description

Title :  STRUCTURE OF RETROMER VPS26-VPS35 SUBUNITS BOUND TO SNX3 AND DMT1 (SEMET LABELED)
 
Authors :  M. Lucas, D. Gershlick, A. Vidaurrazaga, A. L. Rojas, J. S. Bonifacino,
Date :  27 Nov 15  (Deposition) - 07 Dec 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein Transport, Retromer, Sorting Nexin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lucas, D. C. Gershlick, A. Vidaurrazaga, A. L. Rojas, J. S. Bonifacino, A. Hierro
Structural Mechanism For Cargo Recognition By The Retromer Complex.
Cell V. 167 1623 2016
PubMed-ID: 27889239  |  Reference-DOI: 10.1016/J.CELL.2016.10.056

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 35
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGST-PARALLEL2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 14-470
    Gene: VPS35, MEM3, TCCCTA00141
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HVPS35,MATERNAL-EMBRYONIC 3,VESICLE PROTEIN SORTING 35
 
Molecule 2 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO3
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VPS26A, VPS26
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VESICLE PROTEIN SORTING 26A,HVPS26
 
Molecule 3 - SORTING NEXIN-3
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHIS-MBP-PARALLEL2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 14-470
    Gene: SNX3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN SDP3
 
Molecule 4 - NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 2
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO3
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 549-560
    Gene: SLC11A2, DCT1, DMT1, NRAMP2, OK/SW-CL.20
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NRAMP 2,DIVALENT CATION TRANSPORTER 1,DIVALENT METAL TRANSPORTER 1,DMT-1,SOLUTE CARRIER FAMILY 11 MEMBER 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 31)

Asymmetric/Biological Unit (4, 31)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2GOL5Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO46Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:54binding site for residue SO4 A 501
02AC2SOFTWARETYR A:100 , ALA A:101 , GLY A:102binding site for residue SO4 A 502
03AC3SOFTWARELYS A:38 , LEU A:39 , MET A:40 , ASP A:41binding site for residue GOL A 503
04AC4SOFTWARELYS A:120 , CYS A:156 , ASN A:159binding site for residue GOL A 504
05AC5SOFTWAREARG A:54 , ILE A:105 , GLU B:234 , ASP B:237binding site for residue EDO A 505
06AC6SOFTWAREARG A:254 , GLU A:288 , HIS A:290binding site for residue EDO A 506
07AC7SOFTWARESER A:56 , HIS A:142binding site for residue EDO A 507
08AC8SOFTWAREARG A:365binding site for residue EDO A 508
09AC9SOFTWARETYR B:118 , ASP B:263 , VAL B:264 , ASN B:265 , LYS B:266binding site for residue SO4 B 401
10AD1SOFTWAREPRO B:158 , ASP B:159 , VAL B:160 , LYS B:184binding site for residue GOL B 402
11AD2SOFTWARELYS B:38 , HIS B:39 , TYR B:40 , TYR B:147 , ASP B:148binding site for residue EDO B 403
12AD3SOFTWAREARG B:69 , GLU B:94 , VAL B:137binding site for residue EDO B 404
13AD4SOFTWAREGLU B:77 , LEU B:78 , PHE B:79 , ASN B:80 , ALA B:124 , ARG B:127binding site for residue EDO B 405
14AD5SOFTWAREILE B:216 , ASP B:263 , PHE B:268 , SER B:269binding site for residue EDO B 406
15AD6SOFTWAREGLN B:153 , LEU B:154 , ALA B:155 , PRO B:259 , TRP B:295 , ARG B:296binding site for residue EDO B 407
16AD7SOFTWARELYS B:214binding site for residue EDO B 408
17AD8SOFTWARETYR B:157 , LYS B:182 , HIS B:186binding site for residue EDO B 409
18AD9SOFTWAREPHE C:46 , ARG C:70 , TYR C:71 , SER C:72 , SO4 C:202binding site for residue SO4 C 201
19AE1SOFTWARELYS C:95 , ALA C:96 , GLN C:100 , ILE C:109 , ARG C:118 , SO4 C:201binding site for residue SO4 C 202
20AE2SOFTWARESER C:34 , ASN C:35 , PRO C:36 , LYS C:119binding site for residue SO4 C 203
21AE3SOFTWARELEU B:199 , ARG B:201 , LYS B:242 , SER C:26binding site for residue GOL C 204
22AE4SOFTWARELEU C:62 , LYS C:63binding site for residue GOL C 205
23AE5SOFTWAREARG C:99 , LEU C:101 , ASP C:106binding site for residue EDO C 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F0M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F0M)

(-) Exons   (0, 0)

(no "Exon" information available for 5F0M)

(-) 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:458
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f0m A  12 GSKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYMAISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLALFAHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQ 469
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461        


Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......eeeee.hhh.eeeeeee.....eeeeeeeee..........eeeeeeeeeeee..hhhhheeeeeeeeeee........eeeeeee.........ee...eeeeeeeeeeee.....eeeeeeeee............eeeeeee...eeeeeee...eee...eeeeeeeeeee...eeeeeeeeeeeeee......eeeeeeeeeeeeee.......eeeeeee.hhhh....eeee...eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f0m B   8 FGPICEIDIVLNDGETRKmAEmKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFmQVEKPYESYIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKmEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHmELQLIKKEITGIGPSTTTETETIAKYEImDGAPVKGESIPIRLFLAGYDPTPTmRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPE 300
                                    17        27 |      37        47        57        67        77        87        97       107    |  117       127       137       147       157       167       177       187       197       207       217       227       237       247       257   |   267       277       287       297   
                                             26-MSE                                                                               112-MSE                                               166-MSE                                  207-MSE                      236-MSE                  261-MSE                                   
                                                29-MSE                                                                                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhh.....eeeeeeeeeee......eeeeeeeeee........eeeeeeehhhhhhhhhhhhhhh...........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f0m C   4 TVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDEIIDKS 153
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153


Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...eee.ee.. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5f0m D 551 QPELYLLNTmS 561
                                   560 
                                   560-MSE
   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 5F0M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F0M)

(-) Gene Ontology  (127, 167)

Asymmetric/Biological Unit(hide GO term definitions)

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  5f0m
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  NRAM2_HUMAN | P49281
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  SNX3_HUMAN | O60493
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  VP26A_HUMAN | O75436
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  VPS35_HUMAN | Q96QK1
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 Related Entries

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

UniProtKB/Swiss-Prot
        NRAM2_HUMAN | P49281: 5f0l 5f0p
        SNX3_HUMAN | O60493: 2mxc 2yps 5f0j 5f0l 5f0p
        VP26A_HUMAN | O75436: 2fau 5f0j 5f0l 5f0p
        VPS35_HUMAN | Q96QK1: 2r17 5f0j 5f0k 5f0l 5f0p

(-) Related Entries Specified in the PDB File

2fau 2r17 5f0j 5f0k 5f0l