4FME - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ESPG-RAB1-ARF6 COMPLEX

Authors :   F. Shao, Y. Zhu

Date :   16 Jun 12 (Deposition) - 05 Sep 12 (Release) - 03 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.10

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Alpha-Beta Fold, Rab1-Gap, Arf6 Effector, Rab1, Arf6, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Dong, Y. Zhu, Q. Lu, L. Hu, Y. Zheng, F. Shao
Structurally Distinct Bacterial Tbc-Like Gaps Link Arf Gtpase To Rab1 Inactivation To Counteract Host Defenses.
Cell(Cambridge, Mass. ) V. 150 1029 2012
PubMed-ID: 22939626 | Reference-DOI: 10.1016/J.CELL.2012.06.050

Molecule 1 - ESPG PROTEIN
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ESPG
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	O157

Molecule 2 - RAS-RELATED PROTEIN RAB-1A
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RAB1, RAB1A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	YPT1-RELATED PROTEIN

Molecule 3 - ADP-RIBOSYLATION FACTOR 6
	Chains	:	C, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PALSMID
	Gene	:	ARF6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	AF3	2	Ligand/Ion	ALUMINUM FLUORIDE
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
4	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	AF3	1	Ligand/Ion	ALUMINUM FLUORIDE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	AF3	1	Ligand/Ion	ALUMINUM FLUORIDE
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:208 , HOH A:401 , SER B:20 , GLY B:21 , LYS B:24 , THR B:43 , GDP B:202 , MG B:203 , HOH B:301	BINDING SITE FOR RESIDUE AF3 B 201
02	AC2	SOFTWARE	ARG A:208 , THR A:239 , ASP B:19 , GLY B:21 , VAL B:22 , GLY B:23 , LYS B:24 , SER B:25 , CYS B:26 , TYR B:36 , GLU B:38 , ASN B:124 , LYS B:125 , ASP B:127 , LEU B:128 , SER B:154 , ALA B:155 , LYS B:156 , AF3 B:201 , MG B:203 , HOH B:301	BINDING SITE FOR RESIDUE GDP B 202
03	AC3	SOFTWARE	SER B:25 , THR B:43 , ASP B:66 , AF3 B:201 , GDP B:202 , HOH B:301	BINDING SITE FOR RESIDUE MG B 203
04	AC4	SOFTWARE	LEU C:21 , ASP C:22 , ALA C:23 , ALA C:24 , GLY C:25 , LYS C:26 , THR C:27 , THR C:28 , THR C:41 , PRO C:43 , THR C:44 , GLY C:65 , GLY C:66 , ASN C:122 , LYS C:123 , ASP C:125 , LEU C:126 , CYS C:155 , ALA C:156 , THR C:157 , MG C:202	BINDING SITE FOR RESIDUE GTP C 201
05	AC5	SOFTWARE	THR C:27 , THR C:44 , GTP C:201	BINDING SITE FOR RESIDUE MG C 202
06	AC6	SOFTWARE	ARG D:208 , HOH D:401 , SER E:20 , GLY E:21 , LYS E:24 , THR E:43 , GDP E:202 , MG E:203 , HOH E:301	BINDING SITE FOR RESIDUE AF3 E 201
07	AC7	SOFTWARE	ARG D:208 , THR D:239 , ASP E:19 , GLY E:21 , VAL E:22 , GLY E:23 , LYS E:24 , SER E:25 , CYS E:26 , TYR E:36 , GLU E:38 , ASN E:124 , LYS E:125 , ASP E:127 , LEU E:128 , SER E:154 , ALA E:155 , LYS E:156 , AF3 E:201 , MG E:203 , HOH E:301	BINDING SITE FOR RESIDUE GDP E 202
08	AC8	SOFTWARE	SER E:25 , THR E:43 , ASP E:66 , AF3 E:201 , GDP E:202 , HOH E:301	BINDING SITE FOR RESIDUE MG E 203
09	AC9	SOFTWARE	LEU F:21 , ASP F:22 , ALA F:23 , ALA F:24 , GLY F:25 , LYS F:26 , THR F:27 , THR F:28 , THR F:41 , PRO F:43 , THR F:44 , GLY F:65 , GLY F:66 , ASN F:122 , LYS F:123 , ASP F:125 , LEU F:126 , CYS F:155 , ALA F:156 , THR F:157 , MG F:202	BINDING SITE FOR RESIDUE GTP F 201
10	BC1	SOFTWARE	THR F:27 , THR F:44 , GTP F:201	BINDING SITE FOR RESIDUE MG F 202

(no "SS Bond" information available for 4FME)

(no "Cis Peptide Bond" information available for 4FME)

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

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

(no "Exon" information available for 4FME)

Asymmetric 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......hhhhhhhhhhhh..eee.....eeeeeeee.....eeeeeee....eeeee.......eeeee......hhhhh...ee.....eeee........hhhhhhhhhhhhh...eee...................hhhhhh......eee..eeehhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee.....eeeeeeeeeeee........eeeeeeeeeee.........hhhhhhh..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fme A  47 EMSCAEKLLKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLRISVTNSESIEAEIRTPNNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDTTSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANAQMLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATAICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGVLIMAPEDRPNEMGMLTNRTSYEVPQGVKCTIDEMVRALQPRYAASETYLQN 397
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396

Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee........hhhhhhhhh............eeee...ee....eeeeeeeee..hhhhhhhhhhhh....ee..eee..hhhhhhhhhhhhhhhhhhh....ee..eee...hhhhh..hhhhhhhhhhhh....ee.........hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fme B   6 PEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Chain C from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhh..........eeeeeeee..eeeeeeee......hhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhh.........eeeee.........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fme C  14 MRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY 173
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain D from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......hhhhhhhhhhhh..eee.....eeeeeeee.....eeeeeee....eeeee.......eeeee......hhhhh...ee.....eeee........hhhhhhhhhhhhh...eee...................hhhhhh......eee..eeehhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee.....eeeeeeeeeeee........eeeeeeeeeee.........hhhhhhh..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fme D  47 EMSCAEKLLKVLSFGLWNPTYSRSERQSFQELLTVLEPVYPLPNELGRVSARFSDGSSLRISVTNSESIEAEIRTPNNEKITVLLESNEQNRLLQSLPIDRHMPYIQVHRALSEMDLTDTTSMRNLLGFTSKLSTTLIPHNAQTDPLSGPTPFSSIFMDTCRGLGNAKLSLNGVDIPANAQMLLRDALGLKDTHSSPTRNVIDHGISRHDAEQIARESSGSDKQKAEVVEFLCHPEAATAICSAFYQSFNVPALTLTHERISKASEYNAERSLDTPNACINISISQSSDGNIYVTSHTGVLIMAPEDRPNEMGMLTNRTSYEVPQGVKCTIDEMVRALQPRYAASETYLQN 397
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396

Chain E from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee......hhhhhhhhhhh............eeee...ee....eeeeeeeee..hhhhhhhhhhhh....ee..eee..hhhhhhhhhhhhhhhhhhh....ee..eee...hhhhh..hhhhhhhhhhhh....ee.........hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fme E   6 PEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Chain F from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhh..........eeeeeeee..eeeeeeee......hhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhh.........eeeee.........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fme F  14 MRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY 173
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Legend:		→ Mismatch	(orange background)
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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 4FME)

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

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

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4fme)

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	4fme
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UniProtKB/Swiss-Prot
	ARF6_HUMAN \| P62330	:	1e0s 2a5d 2a5f 2a5g 2bao 2bau 2j5x 2w83 3lvq 3lvr 3n5c 3pcr 4kax
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Ligands, Modified Residues, Ions (4, 10)

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