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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF RETROMER VPS26-VPS35 SUBUNITS BOUND TO SNX3

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 :   2.70

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Protein Transport, Retromer, Sorting Nexin, Transport Protein (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

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	:	PMR101A
	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
	Gene	:	SNX3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN SDP3

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 43)

No.	Name	Count	Type	Full Name
1	EDO	24	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	5	Ligand/Ion	GLYCEROL
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (35, 35)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:54	binding site for residue SO4 A 501
02	AC2	SOFTWARE	ALA A:101 , GLY A:102 , HOH A:607	binding site for residue SO4 A 502
03	AC3	SOFTWARE	LYS A:38 , LEU A:39 , MET A:40 , ASP A:41	binding site for residue GOL A 503
04	AC4	SOFTWARE	ARG A:54 , ILE A:105 , GLU B:234 , ASP B:237	binding site for residue EDO A 504
05	AC5	SOFTWARE	GLN A:155 , ARG A:158 , ARG A:226 , GLN A:229	binding site for residue EDO A 505
06	AC6	SOFTWARE	CYS A:137 , VAL A:140 , GLN A:141 , ARG A:150 , GLU A:189 , LYS A:192	binding site for residue EDO A 506
07	AC7	SOFTWARE	ASN A:294 , LYS A:296	binding site for residue EDO A 507
08	AC8	SOFTWARE	ARG A:254 , HIS A:290	binding site for residue EDO A 508
09	AC9	SOFTWARE	ASP A:304 , SER A:349 , VAL A:352 , ASN A:356 , ARG A:400	binding site for residue EDO A 509
10	AD1	SOFTWARE	ARG A:365 , TYR A:368	binding site for residue EDO A 510
11	AD2	SOFTWARE	HOH A:607	binding site for residue EDO A 511
12	AD3	SOFTWARE	LYS A:120 , ASN A:159	binding site for residue EDO A 512
13	AD4	SOFTWARE	TYR B:118 , ASP B:263 , VAL B:264 , ASN B:265	binding site for residue SO4 B 401
14	AD5	SOFTWARE	PRO B:158 , ASP B:159 , VAL B:160 , LYS B:184	binding site for residue GOL B 402
15	AD6	SOFTWARE	ASN B:275 , ARG B:285 , PHE B:287 , GLU B:326	binding site for residue GOL B 403
16	AD7	SOFTWARE	ASP B:81 , ASN B:84 , TYR B:157 , LYS B:182 , HIS B:186	binding site for residue GOL B 404
17	AD8	SOFTWARE	THR B:156	binding site for residue EDO B 405
18	AD9	SOFTWARE	HIS B:39 , TYR B:40 , TYR B:147 , ASP B:148	binding site for residue EDO B 406
19	AE1	SOFTWARE	ARG B:69 , GLU B:94	binding site for residue EDO B 407
20	AE2	SOFTWARE	LYS B:213 , GLU B:215 , GLU B:226 , GLU B:228	binding site for residue EDO B 408
21	AE3	SOFTWARE	GLU B:77 , LEU B:78 , PHE B:79 , ASN B:80 , ALA B:124 , ASN B:125 , VAL B:126 , ARG B:127	binding site for residue EDO B 409
22	AE4	SOFTWARE	ILE B:216 , GLY B:218 , ASP B:263 , SER B:269	binding site for residue EDO B 410
23	AE5	SOFTWARE	GLU B:119 , GLN B:153 , PRO B:259 , ARG B:296	binding site for residue EDO B 411
24	AE6	SOFTWARE	LYS B:82 , ASN B:162 , SER B:163 , EDO B:414	binding site for residue EDO B 412
25	AE7	SOFTWARE	ARG B:139	binding site for residue EDO B 413
26	AE8	SOFTWARE	ASN B:80 , ASN B:161 , ASN B:162 , EDO B:412	binding site for residue EDO B 414
27	AE9	SOFTWARE	LYS B:214 , THR B:225	binding site for residue EDO B 415
28	AF1	SOFTWARE	ASP A:128 , LYS A:131 , THR C:8 , ARG C:10	binding site for residue EDO C 201
29	AF2	SOFTWARE	ARG C:70 , TYR C:71 , SER C:72 , SO4 C:203 , HOH C:308	binding site for residue SO4 C 202
30	AF3	SOFTWARE	LYS C:95 , ALA C:96 , GLN C:100 , ILE C:109 , ARG C:118 , SO4 C:202	binding site for residue SO4 C 203
31	AF4	SOFTWARE	SER C:34 , ASN C:35 , LYS C:119	binding site for residue SO4 C 204
32	AF5	SOFTWARE	LEU B:199 , ARG B:201 , LYS B:242 , SER C:26	binding site for residue GOL C 205
33	AF6	SOFTWARE	THR C:48 , ARG C:68 , ASP C:73 , ILE C:149	binding site for residue EDO C 206
34	AF7	SOFTWARE	ARG A:204 , ARG C:52	binding site for residue EDO C 207
35	AF8	SOFTWARE	LYS C:63	binding site for residue EDO C 208

(no "SS Bond" information available for 5F0J)

(no "Cis Peptide Bond" information available for 5F0J)

(no "SAP(SNP)/Variant" information available for 5F0J)

(no "PROSITE Motif" information available for 5F0J)

(no "Exon" information available for 5F0J)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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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.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f0j 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.......eeeee.hhh.eeeeeee.....eeeeeeeee......eee..eeeeeeeeeee..hhhhheeeeeeeeeee..eee...eeeeeee.........ee...eeeeeeeeeee......eeeeeeeee............eeeeeee...eeeeeee...eee...eeeeeeeeeee...eeeeeeeeeeeeee......eeeeeeeeeeeeee.......eeeeeee.hhhh....eeee...eeeeeeeeeeeee....eeeeeeeeeee..........eee.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f0j B   8 FGPICEIDIVLNDGETRKmAEmKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFmQVEKPYESYIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKmEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHmELQLIKKEITGIGPSTTTETETIAKYEImDGAPVKGESIPIRLFLAGYDPTPTmRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPESAEQPEmGLVPRG 333
                                    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  ||   327      
                                             26-MSE                                                                               112-MSE                                               166-MSE                                  207-MSE                      236-MSE                  261-MSE                                300|     |      
                                                29-MSE                                                                                                                                                                                                                                                                         321     |      
                                                                                                                                                                                                                                                                                                                                     327-MSE

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........eeeeeehhhhhhhhhhhhhhhh..........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f0j C   4 TVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSK 158
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153

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	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 '\|'

(no "SCOP Domain" information available for 5F0J)

(no "CATH Domain" information available for 5F0J)

(no "Pfam Domain" information available for 5F0J)

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Asymmetric/Biological Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 43)

Sites (35, 35)

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