1PXY - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ACTIN-CROSSLINKING CORE OF ARABIDOPSIS FIMBRIN

Authors :   M. G. Klein, W. Shi, Y. Tseng, D. Wirtz, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   07 Jul 03 (Deposition) - 22 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Calponin Homology, F-Actin-Binding Domain (Abd), F-Actin- Crosslinking, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. G. Klein, W. Shi, U. Ramagopal, Y. Tseng, D. Wirtz, D. R. Kovar, C. J. Staiger, S. C. Almo
Structure Of The Actin Crosslinking Core Of Fimbrin.
Structure V. 12 999 2004
PubMed-ID: 15274920 | Reference-DOI: 10.1016/J.STR.2004.04.010
(for further references see the PDB file header)

Molecule 1 - FIMBRIN-LIKE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX4T-2
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	ACTIN-CROSSLINKING CORE, RESIDUES 123-623
	Mutation	:	YES
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1PXY)

(no "Site" information available for 1PXY)

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

Asymmetric Unit

No.	Residues
1	Leu A:147	-	Pro A:148
2	Pro A:444	-	Pro A:445
3	Leu B:147	-	Pro B:148
4	Pro B:444	-	Pro B:445

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

Asymmetric Unit (2, 11)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CH	PS50021	Calponin homology domain profile.	FIMB1_ARATH	123-240 268-371 392-498 513-621	7	B:123-239 A:268-371 B:268-371 A:392-498 B:392-498 A:513-621 B:513-621
2	ACTININ_2	PS00020	Actinin-type actin-binding domain signature 2.	FIMB1_ARATH	212-236 470-494	4	A:212-236 B:212-236 A:470-494 B:470-494

Biological Unit 1 (2, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CH	PS50021	Calponin homology domain profile.	FIMB1_ARATH	123-240 268-371 392-498 513-621	3	- A:268-371 - A:392-498 - A:513-621 -
2	ACTININ_2	PS00020	Actinin-type actin-binding domain signature 2.	FIMB1_ARATH	212-236 470-494	2	A:212-236 - A:470-494 -

Biological Unit 2 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CH	PS50021	Calponin homology domain profile.	FIMB1_ARATH	123-240 268-371 392-498 513-621	4	B:123-239 - B:268-371 - B:392-498 - B:513-621
2	ACTININ_2	PS00020	Actinin-type actin-binding domain signature 2.	FIMB1_ARATH	212-236 470-494	2	- B:212-236 - B:470-494

(no "Exon" information available for 1PXY)

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:465
 aligned with FIMB1_ARATH | Q7G188 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:500
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623
          FIMB1_ARATH   124 SEKGPFVQHINRYLGDDPFLKQFLPLDPHSNQLYELVKDGVLLCKLINVAVPGTIDERAINTKRVLNPWERNENHTLCLNSAKAVGCSVVNIGTQDLAEGRPHLVLGLISQLIKIQVLADLNLKKTPQLVELLEDSDDVEELLRLPPEKVLLKWMNFHLKKGGYKKTVSNFSADLKDAQAYAFLLNVLAPEHCDPATLDAKDPLERAELVLSHAERMNCKRYLTAEEIVEGSSTLNLAFVAQIFHERNGLNKDGKYAFAEMMTEDVETCRDERCYRLWINSLGIDSYVNNVFEDVRNGWILLEVLDKVSPSSVNWKHASKPPIKMPFRKVENCNQVIKIGKQLKFSLVNVAGNDIVQGNKKLILGLLWQLMRFHMLQLLKSLRSRTLGKEMTDADILSWANRKVRTMGRKLQIESFKDKSLSSGLFFLNLLWAVEPRVVNWNLVTKGETDDEKRLNATYIVSVARKLGCSVFLLPEDIVEVNQKMILILTASIMYWSLQR 623
               SCOP domains d1pxya_ A: Fimbrin (Plastin), actin-crosslinking domain                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1pxyA01 A:124-248 Actin-binding Protein, T-fimbrin; domain 1                                                                 -----------------1pxyA02 A:266-374 Actin-binding Protein, T-fimbrin; domain 1                                                 -------------1pxyA03 A:388-507 Actin-binding Protein, T-fimbrin; domain 1                                                            -----1pxyA04 A:513-623 Actin-binding Protein, T-fimbrin; domain 1                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...............hhhhhhh..hhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......-----------------...hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhhh....-------------.hhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...-----..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.....hhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CH  PDB: - UniProt: 123-240                                                                                          ---------------------------CH  PDB: A:268-371 UniProt: 268-371                                                                     --------------------CH  PDB: A:392-498 UniProt: 392-498                                                                        --------------CH  PDB: A:513-621 UniProt: 513-621                                                                          -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------ACTININ_2  PDB: A:212-236-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTININ_2  PDB: A:470-494--------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pxy A 124 SEKGPFVQHINRYLGDDPFLKQFLPLDPHSNQLYELVKDGVLLCKLINVAVPGTIDERAINTKRVLNPWERNENHTLCLNSAKAVGCSVVNIGTQDLAEGRPHLVLGLISQLIKIQLLADLNLKK-----------------LRLPPEKVLLKWMNFHLKKGGYKKTVSNFSADLKDAQAYAFLLNVLAPEHCDPATLDAKDPLERAELVLSHAERMNCKRYLTAEEIVEGSSTLNLAFVAQIFHERNGLN-------------DVETCRDERCYRLWINSLGIDSYVNNVFEDVRNGWILLEVLDKVSPSSVNWKHASKPPIKMPFRKVENCNQVIKIGKQLKFSLVNVAGNDIVQGNKKLILGLLWQLMRFHMLQLLKSLRS-----EMTDADILSWANRKVRTMGRKLQIESFKDKSLSSGLFFLNLLWAVEPRVVNWNLVTKGETDDEKRLNATYIVSVARKLGCSVFLLPEDIVEVNQKMILILTASIMYWSLQR 623
                                   133       143       153       163       173       183       193       203       213       223       233       243    |    -         -  |    273       283       293       303       313       323       333       343       353       363       373|        -    |  393       403       413       423       433       443       453       463       473       483       493       503   |   513       523       533       543       553       563       573       583       593       603       613       623
                                                                                                                                                      248               266                                                                                                         374           388                                                                                                                    507   513

Chain B from PDB  Type:PROTEIN  Length:477
 aligned with FIMB1_ARATH | Q7G188 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:501
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622 
          FIMB1_ARATH   123 QSEKGPFVQHINRYLGDDPFLKQFLPLDPHSNQLYELVKDGVLLCKLINVAVPGTIDERAINTKRVLNPWERNENHTLCLNSAKAVGCSVVNIGTQDLAEGRPHLVLGLISQLIKIQVLADLNLKKTPQLVELLEDSDDVEELLRLPPEKVLLKWMNFHLKKGGYKKTVSNFSADLKDAQAYAFLLNVLAPEHCDPATLDAKDPLERAELVLSHAERMNCKRYLTAEEIVEGSSTLNLAFVAQIFHERNGLNKDGKYAFAEMMTEDVETCRDERCYRLWINSLGIDSYVNNVFEDVRNGWILLEVLDKVSPSSVNWKHASKPPIKMPFRKVENCNQVIKIGKQLKFSLVNVAGNDIVQGNKKLILGLLWQLMRFHMLQLLKSLRSRTLGKEMTDADILSWANRKVRTMGRKLQIESFKDKSLSSGLFFLNLLWAVEPRVVNWNLVTKGETDDEKRLNATYIVSVARKLGCSVFLLPEDIVEVNQKMILILTASIMYWSLQR 623
               SCOP domains d1pxyb_ B: Fimbrin (Plastin), actin-crosslinking domain                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1pxyB01 B:123-245 Actin-binding Protein, T-fimbrin; domain 1                                                               1pxyB02 B      :246-374 Actin-binding Protein, T-fimbrin; domain 1                                                                            1pxyB03 B:388-505 Actin-binding Protein, T-fimbrin; domain 1                                                               --1pxyB04 B:513-623 Actin-binding Protein, T-fimbrin; domain 1                                                    CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1pxyB01 B:516-621                                                                                      -- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1pxyB02 B:516-621                                                                                      -- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1pxyB03 B:516-621                                                                                      -- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1pxyB04 B:516-621                                                                                      -- Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1pxyB05 B:516-621                                                                                      -- Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1pxyB06 B:516-621                                                                                      -- Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1pxyB07 B:516-621                                                                                      -- Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1pxyB08 B:516-621                                                                                      -- Pfam domains (8)
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhh.......hhhhhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhh.hhhhhhhhhhhhhhhhhh.............------...hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhh......-------------.hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CH  PDB: B:123-239 UniProt: 123-240                                                                                   ---------------------------CH  PDB: B:268-371 UniProt: 268-371                                                                     --------------------CH  PDB: B:392-498 UniProt: 392-498                                                                        --------------CH  PDB: B:513-621 UniProt: 513-621                                                                          -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------ACTININ_2  PDB: B:212-236-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTININ_2  PDB: B:470-494--------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pxy B 123 QSEKGPFVQHINRYLGDDPFLKQFLPLDPHSNQLYELVKDGVLLCKLINVAVPGTIDERAINTKRVLNPWERNENHTLCLNSAKAVGCSVVNIGTQDLAEGRPHLVLGLISQLIKIQLLADLNLKKTPQLVE------DVEELLRLPPEKVLLKWMNFHLKKGGYKKTVSNFSADLKDAQAYAFLLNVLAPEHCDPATLDAKDPLERAELVLSHAERMNCKRYLTAEEIVEGSSTLNLAFVAQIFHERNGLN-------------DVETCRDERCYRLWINSLGIDSYVNNVFEDVRNGWILLEVLDKVSPSSVNWKHASKPPIKMPFRKVENCNQVIKIGKQLKFSLVNVAGNDIVQGNKKLILGLLWQLMRFHMLQLLKSL-----GKEMTDADILSWANRKVRTMGRKLQIESFKDKSLSSGLFFLNLLWAVEPRVVNWNLVTKGETDDEKRLNATYIVSVARKLGCSVFLLPEDIVEVNQKMILILTASIMYWSLQR 623
                                   132       142       152       162       172       182       192       202       212       222       232       242       252 |     262       272       282       292       302       312       322       332       342       352       362       372 |       -     | 392       402       412       422       432       442       452       462       472       482       492       502  |    512       522       532       542       552       562       572       582       592       602       612       622 
                                                                                                                                                             254    261                                                                                                              374           388                                                                                                                  505   511

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 alpha proteins (14657)

Fold: CH domain-like (55)

Superfamily: Calponin-homology domain, CH-domain (53)

Family: Calponin-homology domain, CH-domain (28)

Protein domain: Fimbrin (Plastin), actin-crosslinking domain (4)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (1)

1a	d1pxya_	A:
1b	d1pxyb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Actin-binding Protein, T-fimbrin; domain 1 (51)

Homologous Superfamily: Actin-binding Protein, T-fimbrin; domain 1 (51)

Thale cress (Arabidopsis thaliana) (1)

1a	1pxyA02	A:266-374
1b	1pxyB02	B:246-374
1c	1pxyB03	B:388-505
1d	1pxyA03	A:388-507
1e	1pxyA04	A:513-623
1f	1pxyB04	B:513-623
1g	1pxyB01	B:123-245
1h	1pxyA01	A:124-248

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CH (43)

Family: CH (43)

Arabidopsis thaliana (Mouse-ear cress) (1)

1a	CH-1pxyB01	B:516-621
1b	CH-1pxyB02	B:516-621
1c	CH-1pxyB03	B:516-621
1d	CH-1pxyB04	B:516-621
1e	CH-1pxyB05	B:516-621
1f	CH-1pxyB06	B:516-621
1g	CH-1pxyB07	B:516-621
1h	CH-1pxyB08	B:516-621

Asymmetric Unit(hide GO term definitions)

Chain A,B (FIMB1_ARATH | Q7G188)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
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.

Asymmetric Unit
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	Cis Peptide Bonds
		Leu A:147 - Pro A:148	[ RasMol ]
		Leu B:147 - Pro B:148	[ RasMol ]
		Pro A:444 - Pro A:445	[ RasMol ]
		Pro B:444 - Pro B:445	[ RasMol ]

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	1pxy
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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (4, 4)

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