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Asym./Biol. Unit (Jmol Viewer)

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

Title :   REFINED STRUCTURE OF ALPHA-BETA TUBULIN FROM ZINC-INDUCED SHEETS STABILIZED WITH TAXOL

Authors :   J. Lowe, H. Li, K. H. Downing, E. Nogales

Date :   20 Jun 01 (Deposition) - 19 Sep 01 (Release) - 11 Jun 14 (Revision)

Method :   ELECTRON CRYSTALLOGRAPHY

Resolution :   3.50

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

Keywords :   Dimer, Gtpase, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Lowe, H. Li, K. H. Downing, E. Nogales
Refined Structure Of Alpha Beta-Tubulin At 3. 5 A Resolution
J. Mol. Biol. V. 313 1045 2001
PubMed-ID: 11700061 | Reference-DOI: 10.1006/JMBI.2001.5077
(for further references see the PDB file header)

Molecule 1 - TUBULIN ALPHA CHAIN
	Chains	:	A
	Organ	:	BRAIN
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 2 - TUBULIN BETA CHAIN
	Chains	:	B
	Organ	:	BRAIN
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 5)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	TA1	1	Ligand/Ion	TAXOL
5	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:283	BINDING SITE FOR RESIDUE ZN A 900
2	AC2	SOFTWARE	GLN A:11 , GLU A:71 , GTP A:500	BINDING SITE FOR RESIDUE MG A 501
3	AC3	SOFTWARE	GLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ALA A:99 , ALA A:100 , ASN A:101 , SER A:140 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , ILE A:171 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , MG A:501 , LEU B:248 , LYS B:254	BINDING SITE FOR RESIDUE GTP A 500
4	AC4	SOFTWARE	GLY B:10 , GLN B:11 , CYS B:12 , GLN B:15 , SER B:140 , GLY B:142 , GLY B:144 , THR B:145 , GLY B:146 , ASP B:179 , ASN B:206 , TYR B:224 , ASN B:228	BINDING SITE FOR RESIDUE GDP B 600
5	AC5	SOFTWARE	VAL B:23 , ASP B:26 , GLU B:27 , HIS B:229 , LEU B:230 , ALA B:233 , SER B:236 , PHE B:272 , PRO B:274 , LEU B:275 , THR B:276 , ARG B:278 , PRO B:360 , ARG B:369 , GLY B:370	BINDING SITE FOR RESIDUE TA1 B 601

(no "SS Bond" information available for 1JFF)

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

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TBB_PIG_001 *	H	37	V	TBB_PIG	---	---	B	H	37	V
2	UniProt	VAR_TBB_PIG_002 *	N	48	S	TBB_PIG	---	---	B	N	50	S
3	UniProt	VAR_TBB_PIG_003 *	S	275	A	TBB_PIG	---	---	B	S	277	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TUBULIN	PS00227	Tubulin subunits alpha, beta, and gamma signature.	TBB_PIG	140-146	1	B:142-148
1	TUBULIN	PS00227	Tubulin subunits alpha, beta, and gamma signature.	TBA1D_BOVIN	142-148	1	A:142-148

(no "Exon" information available for 1JFF)

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:412
 aligned with TBA1D_BOVIN | Q2HJ86 from UniProtKB/Swiss-Prot  Length:452

    Alignment length:438
                                    11        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        
          TBA1D_BOVIN     2 RECISVHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKELIDLVLDRIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGMDS 439
               SCOP domains d1jffa1 A:2-245 Tubulin alpha-sub                          unit                                                                                                                                                                                     d1jffa2 A:246-439 Tubulin alpha-subunit                                                                                                                                                            SCOP domains
               CATH domains 1jffA01 A:2-268  [code=3.40.50.14                          40, no name defined]                                                                                                                                                                                            1jffA02 A:269-383  [code=3.30.1330.20, no name defined]                                                            1jffA03 A:384-439 Helix hairpin bin                      CATH domains
               Pfam domains -Tubulin-1jffA01 A:3-226                                                                                                                                                                                                         ------------------------------------Tubulin_C-1jffA02 A:263-393                                                                                                        ---------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhhhhhhh.......--------------------------....eeeee.hhhhhhhhhhh..........eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh.....eeee............hhhhhhhhhhhhh....eeee.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh........eee...............hhhhhhhhhhh..............eeeeeeeeee..hhhhhhhhhhhhhh.............eeeee.................eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------TUBULIN--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jff A   2 RECISIHVGQAGVQIGNACWELYCLEHGIQPDG--------------------------HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS 439
                                    11        21        31  |      -         -        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        
                                                           34                         61

Chain B from PDB  Type:PROTEIN  Length:426
 aligned with TBB_PIG | P02554 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:426
                                    11        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      
              TBB_PIG     2 REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQD 427
               SCOP domains d1jffb1 B:2-245 Tubulin beta-subunit                                                                                                                                                                                                              d1jffb2 B:246-437 Tubulin beta-subunit                                                                                                                                                   SCOP domains
               CATH domains 1jffB01 B:2-261  [code=3.40.50.1440, no name defined]                                                                                                                                                                                                             1jffB02 B:262-383  [code=3.30.1330.20, no name defined]                                                           1jffB03 B:384-437 Helix hairpin bin                    CATH domains
               Pfam domains -Tubulin-1jffB01 B:3-226                                                                                                                                                                                                       ------------------------------------Tubulin_C-1jffB02 B:263-393                                                                                                -------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhhhhhh..................hhhhhh...........eeeee.hhhhhhhhh..hhhhh.hhh.eee...............hhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhh....eee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh......eeeee................hhhhhhhhh.........hhhhh.eeeeeeeee...hhhhhhhhhhhhhhhh...........eeeeee..........eeeeeee..hhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------V----------S----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------TUBULIN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jff B   2 REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQD 437
                                    11        21        31        41  ||    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353      |371       381       391       401       411       421       431      
                                                                     44|                                                                                                                                                                                                                                                                                                                      360|                                                                    
                                                                      47                                                                                                                                                                                                                                                                                                                       369

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.20, no name defined] (18)

Cattle (Bos taurus) (4)

1a	1jffB02	B:262-383
1b	1jffA02	A:269-383

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1440, no name defined] (23)

Cattle (Bos taurus) (4)

2a	1jffA01	A:2-268
2b	1jffB01	B:2-261

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: Helix hairpin bin (5)

Cattle (Bos taurus) (4)

3a	1jffA03	A:384-439
3b	1jffB03	B:384-437

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Tubulin-like (34)

Family: Tubulin (34)

Bos taurus (Bovine) (7)

Tubulin-1jffA01

A:3-226

Sus scrofa (Pig) (3)

Tubulin-1jffB01

B:3-226

Family: Tubulin_C (11)

Bos taurus (Bovine) (7)

Tubulin_C-1jffA02

A:263-393

Sus scrofa (Pig) (3)

Tubulin_C-1jffB02

B:263-393

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TBA1D_BOVIN | Q2HJ86)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005200	structural constituent of cytoskeleton	The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
	GO:0007017	microtubule-based process	Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

Chain B (TBB_PIG | P02554)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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).
	GO:0005200	structural constituent of cytoskeleton	The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
	GO:0007017	microtubule-based process	Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

Asymmetric/Biological Unit
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1tub	UNREFINED CRYSTALLOGRAPHIC MODEL OF ALPHA-BETA TUBULIN BY ELECTRON CRYSTALLOGRAPHY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

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Exons (0, 0)

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SCOP Domains (4, 4)

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Related Entries Specified in the PDB File