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(-) Description

Title :  STRUCTURE OF RETROMER VPS26-VPS35 SUBUNITS BOUND TO SNX3 AND DMT1
 
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 :  3.20
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 BL21(DE3)
    Expression System Plasmid: PET-SUMO3
    Expression System Taxid: 469008
    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 BL21(DE3)
    Expression System Plasmid: PET-SUMO3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 545-568
    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  (3, 34)

Asymmetric/Biological Unit (3, 34)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL
2GOL6Ligand/IonGLYCEROL
3SO410Ligand/IonSULFATE ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:101 , GLY A:102binding site for residue SO4 A 501
02AC2SOFTWARELEU A:43 , LYS A:44 , SER A:47 , LEU A:97 , ALA A:101binding site for residue SO4 A 502
03AC3SOFTWARELEU A:276 , GLN A:277 , THR A:278 , LEU A:279 , ASN A:280 , ILE A:327 , ASP C:107binding site for residue SO4 A 503
04AC4SOFTWARELYS A:38 , LEU A:39 , MET A:40 , ASP A:41binding site for residue GOL A 504
05AC5SOFTWARELYS A:120 , ASN A:159binding site for residue GOL A 505
06AC6SOFTWARELYS A:296 , ASP A:346binding site for residue EDO A 506
07AC7SOFTWAREARG A:254 , GLU A:288 , HIS A:290binding site for residue EDO A 507
08AC8SOFTWARESER A:353 , ASN A:356binding site for residue EDO A 508
09AC9SOFTWAREARG A:365binding site for residue EDO A 509
10AD1SOFTWAREALA A:188 , GLN A:249 , GLN C:16 , LEU C:18 , ALA C:21binding site for residue EDO A 510
11AD2SOFTWAREARG A:204 , ARG C:52binding site for residue EDO A 511
12AD3SOFTWAREGLY A:102 , ASN A:103 , GLU B:208 , LYS B:232binding site for residue SO4 B 401
13AD4SOFTWARETYR B:118 , ASP B:263 , VAL B:264 , ASN B:265binding site for residue SO4 B 402
14AD5SOFTWAREPRO B:158 , ASP B:159 , VAL B:160 , LYS B:184 , EDO B:408binding site for residue SO4 B 403
15AD6SOFTWAREGLN B:210 , LYS B:232 , ARG B:285 , LEU D:554binding site for residue SO4 B 404
16AD7SOFTWAREASP B:81 , ASN B:84 , TYR B:157 , LYS B:182 , HIS B:186 , ARG C:9binding site for residue GOL B 405
17AD8SOFTWAREHIS B:39 , TYR B:40 , ASP B:148binding site for residue GOL B 406
18AD9SOFTWAREARG A:54 , GLN B:205 , GLU B:234 , ASP B:237binding site for residue EDO B 407
19AE1SOFTWARETHR B:156 , ILE B:293 , SO4 B:403binding site for residue EDO B 408
20AE2SOFTWAREARG B:69 , GLU B:94binding site for residue EDO B 409
21AE3SOFTWAREALA B:124 , LYS B:213 , GLU B:228binding site for residue EDO B 410
22AE4SOFTWAREGLU B:77 , ASN B:80 , ALA B:124 , ARG B:127binding site for residue EDO B 411
23AE5SOFTWAREILE B:216 , GLY B:218 , ASP B:263 , LYS B:267 , SER B:269binding site for residue EDO B 412
24AE6SOFTWAREGLN B:153 , ALA B:155 , PRO B:259 , ARG B:296binding site for residue EDO B 413
25AE7SOFTWAREASN B:80 , LYS B:82 , ASN B:162binding site for residue EDO B 414
26AE8SOFTWAREARG B:139binding site for residue EDO B 415
27AE9SOFTWAREGLU B:177 , LYS B:194 , LYS C:14binding site for residue EDO B 416
28AF1SOFTWAREPHE C:46 , ARG C:70 , TYR C:71 , SER C:72 , ARG C:118 , SO4 C:202binding site for residue SO4 C 201
29AF2SOFTWARELYS C:95 , ALA C:96 , GLN C:100 , ILE C:109 , ARG C:118 , SO4 C:201binding site for residue SO4 C 202
30AF3SOFTWARESER C:34 , ASN C:35 , PRO C:36 , LYS C:119binding site for residue SO4 C 203
31AF4SOFTWARELEU B:199 , ARG B:201 , LYS B:242 , SER C:26binding site for residue GOL C 204
32AF5SOFTWARELYS C:63binding site for residue GOL C 205
33AF6SOFTWAREARG C:99 , GLN C:100 , LEU C:101 , ASP C:106binding site for residue EDO C 206
34AF7SOFTWARETHR C:48 , ARG C:68 , ASP C:73 , ILE C:149binding site for residue EDO C 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F0L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F0L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F0L)

(-) Exons   (0, 0)

(no "Exon" information available for 5F0L)

(-) 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 .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f0l 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.......eeeee.hhh.eeeeeee.....eeeeeeeee......eee..eeeeeeeeeee..hhh.eeeeeeeeeeee..eee...eeeeeee.........ee...eeeeeeeeeee......eeeeeeeee............eeeeeee...eeeeeee...eee...eeeeeeeeeee...eeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.......eeeeeee.hhhh....eeee...eeeeeeeeeeeee....eeee..eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f0l B   8 FGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPEK 301
                                    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    


Chain C from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhh.....eeeeeeeeeee.hhhhheeeeeeeeee........eeeeeeehhhhhhhhhhhhhhh..........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f0l C   4 TVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSK 158
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     


Chain D from PDB  Type:PROTEIN  Length:10
                                          
               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
                 5f0l D 551 QPELYLLNTM 560
                                   560
   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 5F0L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F0L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F0L)

(-) Gene Ontology  (127, 167)

Asymmetric/Biological Unit(hide GO term definitions)

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  5f0l
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  NRAM2_HUMAN | P49281
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 Related Entries

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

UniProtKB/Swiss-Prot
        NRAM2_HUMAN | P49281: 5f0m 5f0p
        SNX3_HUMAN | O60493: 2mxc 2yps 5f0j 5f0m 5f0p
        VP26A_HUMAN | O75436: 2fau 5f0j 5f0m 5f0p
        VPS35_HUMAN | Q96QK1: 2r17 5f0j 5f0k 5f0m 5f0p

(-) Related Entries Specified in the PDB File

2fau 2r17 5f0j 5f0k