3VE2 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   THE 2.1 ANGSTROM CRYSTAL STRUCTURE OF TRANSFERRIN BINDING PROTEIN B (TBPB) FROM SEROGROUP B M982 NEISSERIA MENINGITIDIS

Authors :   C. Calmettes, T. F. Moraes

Date :   06 Jan 12 (Deposition) - 22 Feb 12 (Release) - 05 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.14

Chains :   Asym. Unit : A,B
Biol. Unit 1: A (2x),B (2x)
Biol. Unit 2: A (2x),B (2x)
Biol. Unit 3: A (1x),B (1x)
Biol. Unit 4: A  (1x)
Biol. Unit 5: B  (1x)

Keywords :   Lipoprotein, Transferrin Receptor, Iron Acquisition, Vaccine Candidate, Host Pathogen Interaction, Beta Barrel, Receptor, Transferrin, Outermembrane, Transferrin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Calmettes, J. Alcantara, R. H. Yu, A. B. Schryvers, T. F. Moraes
The Structural Basis Of Transferrin Sequestration By Transferrin-Binding Protein B.
Nat. Struct. Mol. Biol. V. 19 358 2012
PubMed-ID: 22343719 | Reference-DOI: 10.1038/NSMB.2251

Molecule 1 - TRANSFERRIN-BINDING PROTEIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TBPB, TBP2
	Organism Scientific	:	NEISSERIA MENINGITIDIS SEROGROUP B
	Organism Taxid	:	491
	Strain	:	M982
	Synonym	:	TBP-2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A (2x)	B (2x)
Biological Unit 2 (2x)	:	A (2x)	B (2x)
Biological Unit 3 (1x)	:	A (1x)	B (1x)
Biological Unit 4 (1x)	:	A
Biological Unit 5 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 20)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	11	Ligand/Ion	GLYCEROL
3	NA	1	Ligand/Ion	SODIUM ION
4	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 22)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	GOL	10	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 22)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	GOL	10	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 11)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	GOL	5	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 8)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 5 (2, 11)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	GOL	5	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:93 , ASP A:94 , GLY A:95 , SER A:97 , PHE A:150 , SER A:151 , HOH A:801 , HOH A:929 , HOH A:1031 , HOH B:888	BINDING SITE FOR RESIDUE GOL A 701
02	AC2	SOFTWARE	LYS A:194 , ACT A:708 , HOH A:855 , HOH A:923 , PRO B:54	BINDING SITE FOR RESIDUE GOL A 702
03	AC3	SOFTWARE	ARG A:49 , GLU A:92 , ALA A:145 , SER A:146 , GLU A:147 , HOH A:840 , HOH A:943 , HOH A:1013	BINDING SITE FOR RESIDUE GOL A 703
04	AC4	SOFTWARE	ARG A:46 , VAL A:87 , HOH A:816 , HOH A:989	BINDING SITE FOR RESIDUE GOL A 704
05	AC5	SOFTWARE	ASN A:131 , GLN A:133 , LYS A:345 , LYS A:347 , ASP A:348 , LYS A:349 , HOH A:991 , HOH A:992	BINDING SITE FOR RESIDUE GOL A 705
06	AC6	SOFTWARE	HIS A:129 , LYS A:183 , HOH A:1050	BINDING SITE FOR RESIDUE GOL A 706
07	AC7	SOFTWARE	GLU A:69 , ALA A:70 , HOH A:886 , HOH A:997	BINDING SITE FOR RESIDUE SO4 A 707
08	AC8	SOFTWARE	ARG A:50 , TRP A:52 , GLU A:57 , LYS A:207 , ARG A:211 , GOL A:702 , HOH A:820 , HOH A:855 , PRO B:54	BINDING SITE FOR RESIDUE ACT A 708
09	AC9	SOFTWARE	LYS A:207 , ARG A:211 , HOH A:980 , HOH A:981 , HOH A:1022 , TYR B:53 , LYS B:153 , HOH B:873	BINDING SITE FOR RESIDUE GOL B 701
10	BC1	SOFTWARE	ARG B:46 , HOH B:847 , HOH B:1024 , HOH B:1109	BINDING SITE FOR RESIDUE GOL B 702
11	BC2	SOFTWARE	LYS B:193 , LYS B:337 , HOH B:1078	BINDING SITE FOR RESIDUE GOL B 703
12	BC3	SOFTWARE	ASN B:131 , GLN B:133 , LYS B:345 , ASP B:348 , LYS B:349 , HOH B:1076	BINDING SITE FOR RESIDUE GOL B 704
13	BC4	SOFTWARE	HIS B:129 , LYS B:183 , LYS B:347 , HOH B:883	BINDING SITE FOR RESIDUE GOL B 705
14	BC5	SOFTWARE	HOH A:970 , ARG B:50 , TRP B:52 , GLU B:57 , LYS B:194 , ARG B:211 , HOH B:831 , HOH B:875	BINDING SITE FOR RESIDUE SO4 B 706
15	BC6	SOFTWARE	GLY B:178 , LYS B:179 , LYS B:232 , HIS B:273 , HOH B:834 , HOH B:1031 , HOH B:1032 , HOH B:1045 , HOH B:1046 , HOH B:1047 , HOH B:1068	BINDING SITE FOR RESIDUE SO4 B 707
16	BC7	SOFTWARE	TRP B:68 , GLU B:69 , ALA B:70 , HOH B:887	BINDING SITE FOR RESIDUE SO4 B 708
17	BC8	SOFTWARE	GLU B:58 , SER B:59 , GLU B:60	BINDING SITE FOR RESIDUE SO4 B 709
18	BC9	SOFTWARE	TYR A:53 , THR A:303 , ARG B:211 , HOH B:1075	BINDING SITE FOR RESIDUE SO4 B 710
19	CC1	SOFTWARE	THR B:75 , LYS B:82 , HOH B:856 , HOH B:1002	BINDING SITE FOR RESIDUE SO4 B 711
20	CC2	SOFTWARE	TYR B:41 , GLY B:72 , HOH B:941	BINDING SITE FOR RESIDUE NA B 712

Asymmetric Unit

No.	Residues
1	A:483	-	A:484
2	B:483	-	B:484

Asymmetric Unit

No.	Residues
1	Cys A:483	-	Cys A:484
2	Lys A:565	-	Glu A:566
3	Glu A:615	-	Ser A:616
4	Tyr A:656	-	Pro A:657
5	Asn B:270	-	Asp B:271
6	Glu B:302	-	Thr B:303
7	Cys B:483	-	Cys B:484
8	Lys B:565	-	Glu B:566
9	Glu B:615	-	Ser B:616
10	Tyr B:657	-	Pro B:658

(no "SAP(SNP)/Variant" information available for 3VE2)

(no "PROSITE Motif" information available for 3VE2)

(no "Exon" information available for 3VE2)

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:514
 aligned with TBB1_NEIMI | Q09057 from UniProtKB/Swiss-Prot  Length:711

    Alignment length:653
                                    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       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706   
           TBB1_NEIMI    57 DQGGYGFAMRLKRRNWYPGAEESEVKLNESDWEATGLPTKPKELPKRQKSVIEKVETDGDSDIYSSPYLTPSNHQNGSAGNGVNQPKNQATGHENFQYVYSGWFYKHAASEKDFSNKKIKSGDDGYIFYHGEKPSRQLPASGKVIYKGVWHFVTDTKKGQDFREIIQPSKKQGDRYSGFSGDGSEEYSNKNESTLKDDHEGYGFTSNLEVDFGNKKLTGKLIRNNASLNNNTNNDKHTTQYYSLDAQITGNRFNGTATATDKKENETKLHPFVSDSSSLSGGFFGPQGEELGFRFLSDDQKVAVVGSAKTKDKLENGAAASGSTGAAASGGAAGTSSENSKLTTVLDAVELTLNDKKIKNLDNFSNAAQLVVDGIMIPLLPKDSESGNTQADKGKNGGTEFTRKFEHTPESDKKDAQAGTQTNGAQTASNTAGDTNGKTKTYEVEVCCSNLNYLKYGMLTRKNSKSAMQAGGNSSQADAKTEQVEQSMFLQGERTDEKEIPTDQNVVYRGSWYGHIANGTSWSGNASDKEGGNRAEFTVNFADKKITGKLTAENRQAQTFTIEGMIQGNGFEGTAKTAESGFDLDQKNTTRTPKAYITDAKVKGGFYGPKAEELGGWFAYPGDKQTEKATATSSDGNSASSATVVFGAKRQQP 709
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.............ee..hhhhhee..........hhhhhhhhhhh........ee......-------------....ee........eeeeeeee....eee....eee...eeeeeeee.....eee...eeeeeeeeeeee.ee...........................................ee.eeeeeeee....eeeeeeeee....------...eeeeeeeeeeee..eeeeeeee................eeeeeeeee.....eeeeeee.....eeeeeeee....---------------------------.eee.eeeeeee....eeee........eeee..eeee....-----------------....eeee...----------------------------..eeeeeee......eeeeeeeee---------------------.eeeeeeeee..hhhhh.....eeeeeeeeeeee...eeee.........eeeeeee....eeeeeee...----.eeeeeeee..eeeeeee.........-------.......eeeeeeee.....eeeeeeee..----------------..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ve2 A  37 DQGGYGFAMRLKRRNWYPGAEESEVKLNESDWEATGLPTKPKELPKRQKSVIEKVETDGDSDIYSSPYLTP-------------QPKNQATGHENFQYVYSGWFYKHAASEKDFSNKKIKSGDDGYIFYHGEKPSRQLPASGKVIYKGVWHFVTDTKKGQDFREIIQPSKKQGDRYSGFSGDGSEEYSNKNESTLKDDHEGYGFTSNLEVDFGNKKLTGKLIRNNASL------DKHTTQYYSLDAQITGNRFNGTATATDKKENETKLHPFVSDSSSLSGGFFGPQGEELGFRFLSDDQKVAVVGSAKTKDK---------------------------KLTTVLDAVELTLNDKKIKNLDNFSNAAQLVVDGIMIPLLPK-----------------EFTRKFEHTPE----------------------------TKTYEVEVCCSNLNYLKYGMLTRK---------------------VEQSMFLQGERTDEKEIPTDQNVVYRGSWYGHIANGTSWSGNASDKEGGNRAEFTVNFADKKITGKLTAEN----TFTIEGMIQGNGFEGTAKTAESGFDLD-------PKAYITDAKVKGGFYGPKAEELGGWFAYPG----------------ASSATVVFGAKRQQP 689
                                    46        56        66        76        86        96       106|        -    |  126       136       146       156       166       176       186       196       206       216       226       236       246       256       | -    |  276       286       296       306       316       326       336       346  |      -         -         -|      386       396       406       416 |       -       436       446         -         -       476       486       496 |       -         -   |   526       536       546       556       566       576       586   |   596       606       616    |    -  |    636       646       656 |       -       676       686   
                                                                                                107           121                                                                                                                                            264    271                                                                           349                         377                                      418               436       446                          475                    498                   520                                                                   590  595                       621     629                          658              675

Chain B from PDB  Type:PROTEIN  Length:519
 aligned with TBB1_NEIMI | Q09057 from UniProtKB/Swiss-Prot  Length:711

    Alignment length:651
                                    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       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706 
           TBB1_NEIMI    57 DQGGYGFAMRLKRRNWYPGAEESEVKLNESDWEATGLPTKPKELPKRQKSVIEKVETDGDSDIYSSPYLTPSNHQNGSAGNGVNQPKNQATGHENFQYVYSGWFYKHAASEKDFSNKKIKSGDDGYIFYHGEKPSRQLPASGKVIYKGVWHFVTDTKKGQDFREIIQPSKKQGDRYSGFSGDGSEEYSNKNESTLKDDHEGYGFTSNLEVDFGNKKLTGKLIRNNASLNNNTNNDKHTTQYYSLDAQITGNRFNGTATATDKKENETKLHPFVSDSSSLSGGFFGPQGEELGFRFLSDDQKVAVVGSAKTKDKLENGAAASGSTGAAASGGAAGTSSENSKLTTVLDAVELTLNDKKIKNLDNFSNAAQLVVDGIMIPLLPKDSESGNTQADKGKNGGTEFTRKFEHTPESDKKDAQAGTQTNGAQTASNTAGDTNGKTKTYEVEVCCSNLNYLKYGMLTRKNSKSAMQAGGNSSQADAKTEQVEQSMFLQGERTDEKEIPTDQNVVYRGSWYGHIANGTSWSGNASDKEGGNRAEFTVNFADKKITGKLTAENRQAQTFTIEGMIQGNGFEGTAKTAESGFDLDQKNTTRTPKAYITDAKVKGGFYGPKAEELGGWFAYPGDKQTEKATATSSDGNSASSATVVFGAKRQ 707
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.............ee..hhhhhee..........hhhhhhhhhhh........ee........-----..........ee........eeeeeeee....eeehhhheee...eeeeeeee.....eee...eeeeeeeeeeee.ee...........................................ee.eeeeeeee....eeeeeeeee....-----....eeeeeeeeeeee..eeeeeeee................eeeeeeeee.....eeeeeee.....eeeeeeee....--------------------------..eee.eeeeeee....eeee........eeee..eeee...------------------....eeee...----------------------------..eeeeeee......eeeeeeeee---------------------.eeeeeeeee..hhhhh.....eeeeeeeeeeee...eeee.........eeeeeee....eeeeeee..----.eeeeeeeee..eeeeeee........--------.......eeeeeeeehhhh.eeeeeeee.-----------------..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ve2 B  37 DQGGYGFAMRLKRRNWYPGAEESEVKLNESDWEATGLPTKPKELPKRQKSVIEKVETDGDSDIYSSPYLTPSN-----AGNGVNQPKNQATGHENFQYVYSGWFYKHAASEKDFSNKKIKSGDDGYIFYHGEKPSRQLPASGKVIYKGVWHFVTDTKKGQDFREIIQPSKKQGDRYSGFSGDGSEEYSNKNESTLKDDHEGYGFTSNLEVDFGNKKLTGKLIRNNASL-----NDKHTTQYYSLDAQITGNRFNGTATATDKKENETKLHPFVSDSSSLSGGFFGPQGEELGFRFLSDDQKVAVVGSAKTKDK--------------------------SKLTTVLDAVELTLNDKKIKNLDNFSNAAQLVVDGIMIPLLP------------------EFTRKFEHTPE----------------------------TKTYEVEVCCSNLNYLKYGMLTRK---------------------VEQSMFLQGERTDEKEIPTDQNVVYRGSWYGHIANGTSWSGNASDKEGGNRAEFTVNFADKKITGKLTAE----QTFTIEGMIQGNGFEGTAKTAESGFDL--------PKAYITDAKVKGGFYGPKAEELGGWFAYP-----------------ASSATVVFGAKRQ 687
                                    46        56        66        76        86        96       106  |    116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       | -   |   276       286       296       306       316       326       336       346  |      -         -       376       386       396       406       416|        -       436       446         -         -       476       486       496 |       -         -   |   526       536       546       556       566       576       586  |    596       606       616   |     -  |    637       647       657|        -       676       686 
                                                                                                  109   115                                                                                                                                                  264   270                                                                            349                        376                                      417                436       446                          475                    498                   520                                                                  589  594                       620      630                         658               675

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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 3VE2)

(no "CATH Domain" information available for 3VE2)

(no "Pfam Domain" information available for 3VE2)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TBB1_NEIMI | Q09057)


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.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn B:270 - Asp B:271	[ RasMol ]
		Cys A:483 - Cys A:484	[ RasMol ]
		Cys B:483 - Cys B:484	[ RasMol ]
		Glu A:615 - Ser A:616	[ RasMol ]
		Glu B:302 - Thr B:303	[ RasMol ]
		Glu B:615 - Ser B:616	[ RasMol ]
		Lys A:565 - Glu A:566	[ RasMol ]
		Lys B:565 - Glu B:566	[ RasMol ]
		Tyr A:656 - Pro A:657	[ RasMol ]
		Tyr B:657 - Pro B:658	[ RasMol ]

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	3ve2
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	TBB1_NEIMI \| Q09057	:	3ve1

Description

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Ligands, Modified Residues, Ions (4, 20)

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SS Bonds (2, 2)

Cis Peptide Bonds (10, 10)

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