2ZQK - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF INTIMIN-TIR68 COMPLEX

Authors :   Y. Ma, F. Gao, D. -F. Li, G. F. Gao

Date :   12 Aug 08 (Deposition) - 18 Aug 09 (Release) - 18 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D,M,N
Biol. Unit 1: A,M,N  (1x)
Biol. Unit 2: B,C,D  (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)
Biol. Unit 5: M,N  (1x)
Biol. Unit 6: C,D  (1x)

Keywords :   Protein-Protein Complex, Unique Intimin-Tir Trimer Intermediate, Cell Membrane, Cell Outer Membrane, Membrane, Transmembrane, Virulence, Receptor, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Ma, Q. Zou, G. F. Gao
Structural Insight Into The Interaction Between Intimin And Tir Of Enterohaemorrhagic E Coli: Evidence For A Dynamic Sequential Clustering-Aggregating-Reticulating Model
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - INTIMIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	D2-D3 DOMAIN, UNP RESIDUES 747-934
	Gene	:	INTIMIN ADHERENCE PROTEIN 747-934
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83334
	Synonym	:	ATTACHING AND EFFACING PROTEIN, EAE PROTEIN, GAMMA-INTIMIN

Molecule 2 - PUTATIVE TRANSLOCATED INTIMIN RECEPTOR PROTEIN (TRANSLOCATED INTIMIN RECEPTOR TIR)
	Chains	:	M, N, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	IBD DOMAIN, UNP RESIDUES 269-336
	Gene	:	TIR 269-336
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83334

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2ZQK)

(no "Site" information available for 2ZQK)

Asymmetric Unit

No.	Residues
1	A:112	-	A:186
2	B:112	-	B:186

(no "Cis Peptide Bond" information available for 2ZQK)

(no "SAP(SNP)/Variant" information available for 2ZQK)

(no "PROSITE Motif" information available for 2ZQK)

(no "Exon" information available for 2ZQK)

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:183
 aligned with EAE_ECO57 | P43261 from UniProtKB/Swiss-Prot  Length:934

    Alignment length:183
                                   761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931   
            EAE_ECO57   752 FFDELKIDNKVDIIGNNVRGELPNIWLQYGQFKLKASGGDGTYSWYSENTSIATVDASGKVTLNGKGSVVIKATSGDKQTVSYTIKAPSYMIKVDKQAYYADAMSICKNLLPSTQTVLSDIYDSWGAANKYSHYSSMNSITAWIKQTSSEQRSGVSSTYNLITQNPLPGVNVNTPNVYAVCVE 934
               SCOP domains d2zqka1 A:6-94 automated matches                                                         d2zqka2 A:95-188 automated matches                                                             SCOP domains
               CATH domains 2zqkA01 A:6-95  [code=2.60.40.1080, no name defined]                                      2zqkA02 A:96-188 Mannose-Binding Protein A, subunit A                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...eee.....ee.....ee...eee..ee.....eeeee.....eee....eeee.....eeeeeee....eeeeee.....eeeeeee.hhhhhhhhhh......hhhhhhhhhhhhhhhhh.........eeee..hhhhhhhheeeeee...eeeeeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zqk A   6 FFDELKIDNKVDIIGNNVRGELPNIWLQYGQFKLKASGGDGTYSWYSENTSIATVDASGKVTLNGKGSVVIKATSGDKQTVSYTIKAPSYMIKVDKQAYYADAMSICKNLLPSTQTVLSDIYDSWGAANKYSHYSSMNSITAWIKQTSSEQRSGVSSTYNLITQNPLPGVNVNTPNVYAVCVE 188
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with EAE_ECO57 | P43261 from UniProtKB/Swiss-Prot  Length:934

    Alignment length:184
                                   760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930    
            EAE_ECO57   751 TFFDELKIDNKVDIIGNNVRGELPNIWLQYGQFKLKASGGDGTYSWYSENTSIATVDASGKVTLNGKGSVVIKATSGDKQTVSYTIKAPSYMIKVDKQAYYADAMSICKNLLPSTQTVLSDIYDSWGAANKYSHYSSMNSITAWIKQTSSEQRSGVSSTYNLITQNPLPGVNVNTPNVYAVCVE 934
               SCOP domains d2zqkb1 B:5-94 automated matches                                                          d2zqkb2 B:95-188 automated matches                                                             SCOP domains
               CATH domains 2zqkB01 B:5-95  [code=2.60.40.1080, no name defined]                                       2zqkB02 B:96-188 Mannose-Binding Protein A, subunit A                                         CATH domains
           Pfam domains (1) -------Big_2-2zqkB03 B:12-90                                                          --Intimin_C-2zqkB01 B:93-188                                                                       Pfam domains (1)
           Pfam domains (2) -------Big_2-2zqkB04 B:12-90                                                          --Intimin_C-2zqkB02 B:93-188                                                                       Pfam domains (2)
         Sec.struct. author ......ee...eee.....ee...........ee..ee.....eeeee.....eee.....eee.....eeeeeee....eeeeee.......eeeee.hhhhhhhhh.......hhhhhhhhhhh.hhhhh.........eeee..hhhhhhh.eeeeee...eeeeeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zqk B   5 TFFDELKIDNKVDIIGNNVRGELPNIWLQYGQFKLKASGGDGTYSWYSENTSIATVDASGKVTLNGKGSVVIKATSGDKQTVSYTIKAPSYMIKVDKQAYYADAMSICKNLLPSTQTVLSDIYDSWGAANKYSHYSSMNSITAWIKQTSSEQRSGVSSTYNLITQNPLPGVNVNTPNVYAVCVE 188
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184

Chain C from PDB  Type:PROTEIN  Length:64
 aligned with TIR_ECO57 | Q7DB77 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:64
                                   282       292       302       312       322       332    
            TIR_ECO57   273 SATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN 336
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...eeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2zqk C   5 SATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN  68
                                    14        24        34        44        54        64

Chain D from PDB  Type:PROTEIN  Length:63
 aligned with TIR_ECO57 | Q7DB77 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:63
                                   283       293       303       313       323       333   
            TIR_ECO57   274 ATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN 336
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.....eeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2zqk D   6 ATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN  68
                                    15        25        35        45        55        65

Chain M from PDB  Type:PROTEIN  Length:64
 aligned with TIR_ECO57 | Q7DB77 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:64
                                   282       292       302       312       322       332    
            TIR_ECO57   273 SATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN 336
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2zqk M   5 SATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN  68
                                    14        24        34        44        54        64

Chain N from PDB  Type:PROTEIN  Length:63
 aligned with TIR_ECO57 | Q7DB77 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:63
                                   283       293       303       313       323       333   
            TIR_ECO57   274 ATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN 336
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2zqk N   6 ATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN  68
                                    15        25        35        45        55        65

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Invasin/intimin cell-adhesion fragments (9)

Family: automated matches (5)

Protein domain: automated matches (5)

Escherichia coli [TaxId: 83334] (1)

1a	d2zqka1	A:6-94
1b	d2zqkb1	B:5-94

Class: Alpha and beta proteins (a+b) (23004)

Fold: C-type lectin-like (322)

Superfamily: C-type lectin-like (322)

Family: automated matches (88)

Protein domain: automated matches (88)

Escherichia coli [TaxId: 83334] (2)

2a	d2zqka2	A:95-188
2b	d2zqkb2	B:95-188

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C_Lectin (98)

Family: Intimin_C (2)

Escherichia coli O157:H7 (2)

1a	Intimin_C-2zqkB01	B:93-188
1b	Intimin_C-2zqkB02	B:93-188

Clan: E-set (290)

Family: Big_2 (2)

Escherichia coli O157:H7 (2)

2a	Big_2-2zqkB03	B:12-90
2b	Big_2-2zqkB04	B:12-90

Asymmetric Unit(hide GO term definitions)

Chain A,B (EAE_ECO57 | P43261)

biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain C,D,M,N (TIR_ECO57 | Q7DB77)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	EAE_ECO57 \| P43261	:	2zwk 3ncw 3ncx 4e1s 5g26
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2zwk	INTIMIN-TIR90 COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

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SCOP Domains (2, 4)

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