1ZRO - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF EBA-175 REGION II (RII) CRYSTALLIZED IN THE PRESENCE OF (ALPHA)2,3-SIALYLLACTOSE

Authors :   N. H. Tolia, E. J. Enemark, B. K. Sim, L. Joshua-Tor

Date :   19 May 05 (Deposition) - 09 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Eba-175, Rii, Dbl, Erythrocyte, Invasion, Host, Malaria, Disease, Glycophorin, Glycan, Sialic Acid, Binding, Sialyllactose, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. H. Tolia, E. J. Enemark, B. K. Sim, L. Joshua-Tor
Structural Basis For The Eba-175 Erythrocyte Invasion Pathway Of The Malaria Parasite Plasmodium Falciparum.
Cell(Cambridge, Mass. ) V. 122 183 2005
PubMed-ID: 16051144 | Reference-DOI: 10.1016/J.CELL.2005.05.033
(for further references see the PDB file header)

Molecule 1 - ERYTHROCYTE BINDING ANTIGEN REGION II
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Mutation	:	YES
	Organism Common	:	MALARIA PARASITE P. FALCIPARUM
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833
	Synonym	:	EBA-175 REGION II (RII)

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 20)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	SO4	16	Ligand/Ion	SULFATE ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:417 , ARG A:422 , HOH A:859 , LYS B:28 , ASN B:29 , ARG B:31 , HOH B:721 , HOH B:784	BINDING SITE FOR RESIDUE SO4 B 701
02	AC2	SOFTWARE	THR A:54 , TYR A:55 , THR A:56 , THR A:59 , HOH A:996	BINDING SITE FOR RESIDUE SO4 A 702
03	AC3	SOFTWARE	ARG A:407 , TRP A:450 , LYS A:454 , HOH A:861	BINDING SITE FOR RESIDUE SO4 A 703
04	AC4	SOFTWARE	VAL A:329 , TRP A:330 , ASP A:496 , TRP A:528 , LYS A:531 , LYS A:532 , HOH A:837 , HOH A:845 , HOH A:910	BINDING SITE FOR RESIDUE SO4 A 704
05	AC5	SOFTWARE	LYS A:53 , GLY A:110 , GLY A:111 , HOH A:869 , HOH A:991 , HOH A:1006	BINDING SITE FOR RESIDUE SO4 A 705
06	AC6	SOFTWARE	ARG A:15 , ARG A:18 , GLN A:43 , HOH A:803 , HOH A:836 , HOH A:838	BINDING SITE FOR RESIDUE SO4 A 706
07	AC7	SOFTWARE	ASN A:438 , LYS A:439 , HOH A:992	BINDING SITE FOR RESIDUE SO4 A 707
08	AC8	SOFTWARE	TRP A:458 , LYS A:468 , CYS A:471 , LYS A:472 , GLU A:473 , HOH A:858	BINDING SITE FOR RESIDUE SO4 A 708
09	AC9	SOFTWARE	ARG A:437	BINDING SITE FOR RESIDUE CL A 710
10	BC1	SOFTWARE	LYS A:28 , ASN A:29 , ARG A:31 , HOH A:753 , HOH A:986 , ASN B:417 , ARG B:422 , HOH B:893	BINDING SITE FOR RESIDUE SO4 A 711
11	BC2	SOFTWARE	HOH A:864 , THR B:54 , TYR B:55 , THR B:56 , THR B:59	BINDING SITE FOR RESIDUE SO4 B 712
12	BC3	SOFTWARE	ARG B:407 , TRP B:450 , LYS B:454 , HOH B:895	BINDING SITE FOR RESIDUE SO4 B 713
13	BC4	SOFTWARE	VAL B:329 , TRP B:330 , ASP B:496 , TRP B:528 , LYS B:531 , LYS B:532 , HOH B:870 , HOH B:878 , HOH B:940	BINDING SITE FOR RESIDUE SO4 B 714
14	BC5	SOFTWARE	LYS B:53 , GLY B:110 , GLY B:111 , HOH B:729 , HOH B:744 , HOH B:902	BINDING SITE FOR RESIDUE SO4 B 715
15	BC6	SOFTWARE	ARG B:15 , ARG B:18 , GLN B:43 , HOH B:835 , HOH B:869 , HOH B:871	BINDING SITE FOR RESIDUE SO4 B 716
16	BC7	SOFTWARE	ASN B:438 , LYS B:439 , HOH B:730	BINDING SITE FOR RESIDUE SO4 B 717
17	BC8	SOFTWARE	TRP B:458 , LYS B:468 , CYS B:471 , LYS B:472 , GLU B:473 , HOH B:892	BINDING SITE FOR RESIDUE SO4 B 718
18	BC9	SOFTWARE	LYS B:150	BINDING SITE FOR RESIDUE CL B 719
19	CC1	SOFTWARE	ARG B:437	BINDING SITE FOR RESIDUE CL B 720

Asymmetric/Biological Unit

No.	Residues
1	A:14	-	A:45
2	A:25	-	A:36
3	A:88	-	A:166
4	A:202	-	A:215
5	A:211	-	A:283
6	A:219	-	A:281
7	A:318	-	A:353
8	A:332	-	A:344
9	A:396	-	A:471
10	A:494	-	A:574
11	A:508	-	A:518
12	A:513	-	A:598
13	A:522	-	A:595
14	B:14	-	B:45
15	B:25	-	B:36
16	B:88	-	B:166
17	B:202	-	B:215
18	B:211	-	B:283
19	B:219	-	B:281
20	B:318	-	B:353
21	B:332	-	B:344
22	B:396	-	B:471
23	B:494	-	B:574
24	B:508	-	B:518
25	B:513	-	B:598
26	B:522	-	B:595

(no "Cis Peptide Bond" information available for 1ZRO)

(no "SAP(SNP)/Variant" information available for 1ZRO)

(no "PROSITE Motif" information available for 1ZRO)

(no "Exon" information available for 1ZRO)

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:588
 aligned with Q25735_PLAFA | Q25735 from UniProtKB/TrEMBL  Length:616

    Alignment length:594
                                    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       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597    
         Q25735_PLAFA     8 NEVLSNCREKRKGMKWDCKKKNDRSNYVCIPDRRIQLCIVNLSIIKTYTKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGEISEHKIKNFRKKWWNEFREKLWEAMLSEHKNNINNCKNIPQEELQITQWIKEWHGEFLLERDNRSKLPKSKCKNNTLYEACEKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIKISENKNDAKVSLLLNNCDAEYSKYCDCKHTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKPYKLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQDKTKMIETLKVECKEKPCEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKCTMCPEV 601
               SCOP domains d1zroa1 A:8-282 Erythrocyte binding antigen region II                                                                                                                                                                                                                              d1zroa2 A:283-601 Erythrocyte binding antigen region II                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh........eeee........eeeehhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......--........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhh.hhhhhhhhh.hhhhhh......eee.........eeehhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh----....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zro A   8 NEVLSNCREKRKGMKWDCKKKNDRSNYVCIPDRRIQLCIVNLAIIKTYTKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGEISEHKIKNFRKKWWNEFREKLWEAMLSEHKNNI--CKNIPQEELQITQWIKEWHGEFLLERDNRAKLPKSKCKNNALYEACEKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIKISENKNDAKVSLLLNNCDAEYSKYCDCKHTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKPYKLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQDKTKMIETLKVEC----CEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKCTMCPEV 601
                                    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       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507|    | 517       527       537       547       557       567       577       587       597    
                                                                                                                                                                                     163  |                                                                                                                                                                                                                                                                                                                                                   508  513                                                                                        
                                                                                                                                                                                        166

Chain B from PDB  Type:PROTEIN  Length:588
 aligned with Q25735_PLAFA | Q25735 from UniProtKB/TrEMBL  Length:616

    Alignment length:594
                                    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       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597    
         Q25735_PLAFA     8 NEVLSNCREKRKGMKWDCKKKNDRSNYVCIPDRRIQLCIVNLSIIKTYTKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGEISEHKIKNFRKKWWNEFREKLWEAMLSEHKNNINNCKNIPQEELQITQWIKEWHGEFLLERDNRSKLPKSKCKNNTLYEACEKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIKISENKNDAKVSLLLNNCDAEYSKYCDCKHTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKPYKLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQDKTKMIETLKVECKEKPCEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKCTMCPEV 601
               SCOP domains d1zrob1 B:8-282 Erythrocyte binding antigen region II                                                                                                                                                                                                                              d1zrob2 B:283-601 Erythrocyte binding antigen region II                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------  --------------------------------------------------------------------------------------------------------------------------------------------------------Duffy_binding-1zroB01 B:318-566                                                                                                                                                                                                                          ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------  --------------------------------------------------------------------------------------------------------------------------------------------------------Duffy_binding-1zroB02 B:318-566                                                                                                                                                                                                                          ----------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------  --------------------------------------------------------------------------------------------------------------------------------------------------------Duffy_binding-1zroB03 B:318-566                                                                                                                                                                                                                          ----------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------  --------------------------------------------------------------------------------------------------------------------------------------------------------Duffy_binding-1zroB04 B:318-566                                                                                                                                                                                                                          ----------------------------------- Pfam domains (4)
         Sec.struct. author .hhhhhh........eeee........eeeehhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......--........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhh.hhhhhhhhh.hhhhhh......eee.........eeehhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh----....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zro B   8 NEVLSNCREKRKGMKWDCKKKNDRSNYVCIPDRRIQLCIVNLAIIKTYTKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFLDYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGEISEHKIKNFRKKWWNEFREKLWEAMLSEHKNNI--CKNIPQEELQITQWIKEWHGEFLLERDNRAKLPKSKCKNNALYEACEKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIKISENKNDAKVSLLLNNCDAEYSKYCDCKHTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKPYKLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYWNDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQDKTKMIETLKVEC----CEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKCTMCPEV 601
                                    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       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507|    | 517       527       537       547       557       567       577       587       597    
                                                                                                                                                                                     163  |                                                                                                                                                                                                                                                                                                                                                   508  513                                                                                        
                                                                                                                                                                                        166

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Duffy binding domain-like (7)

Superfamily: Duffy binding domain-like (7)

Family: Duffy binding domain (6)

Protein domain: Erythrocyte binding antigen region II (2)

Malaria parasite (Plasmodium falciparum) [TaxId: 5833] (2)

1a	d1zroa1	A:8-282
1b	d1zroa2	A:283-601
1c	d1zrob1	B:8-282
1d	d1zrob2	B:283-601

(no "CATH Domain" information available for 1ZRO)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DBL (4)

Family: Duffy_binding (4)

Plasmodium falciparum (3)

1a	Duffy_binding-1zroB01	B:318-566
1b	Duffy_binding-1zroB02	B:318-566
1c	Duffy_binding-1zroB03	B:318-566
1d	Duffy_binding-1zroB04	B:318-566

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q25735_PLAFA | Q25735)

molecular function
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	1zro
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 20)

Sites (19, 19)

SS Bonds (26, 26)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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