4BQK - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   RICE IMPORTIN_ALPHA : VIRD2NLS COMPLEX

Authors :   C. -W. Chang, R. M. Counago, S. J. Williams, B. Kobe

Date :   31 May 13 (Deposition) - 19 Feb 14 (Release) - 18 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Transport Protein, Hydrolase, Nuclear Localization Signal (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. -W. Chang, S. J. Williams, R. M. Counago, B. Kobe
Structural Basis Of Interaction Of Bipartite Nuclear Localization Signal From Agrobacterium Vird2 With Rice Importin-Alpha
Mol. Plant V. 7 1061 2014
PubMed-ID: 24503158 | Reference-DOI: 10.1093/MP/SSU014

Molecule 1 - IMPORTIN SUBUNIT ALPHA-1A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A_RIMPALPHA1A_DIBB
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET30A
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 73-526
	Organism Common	:	RICE
	Organism Scientific	:	ORYZA SATIVA
	Organism Taxid	:	4530

Molecule 2 - T-DNA BORDER ENDONUCLEASE VIRD2
	Chains	:	C, D
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX2T-VIRD2NLS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PGEX2T
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 415-434
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	358
	Synonym	:	VIRD2NLS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	PEG	9	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	PEG	5	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:161 , HOH A:2080 , THR B:336 , PRO B:373 , HOH B:2114 , HOH B:2156	BINDING SITE FOR RESIDUE PEG B1495
2	AC2	SOFTWARE	VAL B:164 , LYS B:165 , LEU B:167 , GLY B:168 , PRO B:204 , ALA B:207 , ILE B:422 , HOH B:2025	BINDING SITE FOR RESIDUE PEG B1496
3	AC3	SOFTWARE	ARG B:230 , TRP B:264 , TYR B:268 , ARG C:430	BINDING SITE FOR RESIDUE PEG B1497
4	AC4	SOFTWARE	PRO B:242 , PRO B:245 , GLU B:468 , GLU B:471 , ASN B:472 , HOH B:2059 , HOH B:2147	BINDING SITE FOR RESIDUE PEG B1498
5	AC5	SOFTWARE	VAL A:164 , LYS A:165 , LEU A:167 , GLY A:168 , PRO A:204 , HOH A:2053 , HOH A:2055 , HOH A:2229	BINDING SITE FOR RESIDUE PEG A1495
6	AC6	SOFTWARE	ASP A:172 , ARG A:175 , GLU A:176 , HIS A:212 , LYS A:214 , MET A:217	BINDING SITE FOR RESIDUE PEG A1496
7	AC7	SOFTWARE	LEU A:209 , ASN A:210 , ALA A:246 , ARG A:249 , HOH A:2084	BINDING SITE FOR RESIDUE PEG A1497
8	AC8	SOFTWARE	ARG A:241 , LEU A:244 , ALA A:279 , ALA A:283	BINDING SITE FOR RESIDUE PEG A1498
9	AC9	SOFTWARE	GLN B:363 , ASP B:403	BINDING SITE FOR RESIDUE PEG B1499

(no "SS Bond" information available for 4BQK)

Asymmetric Unit

No.	Residues
1	Lys A:232	-	Pro A:233
2	Ser B:101	-	Ile B:102
3	Lys B:232	-	Pro B:233

(no "SAP(SNP)/Variant" information available for 4BQK)

Asymmetric Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARM_REPEAT	PS50176	Armadillo/plakoglobin ARM repeat profile.	IMA1A_ORYSJ	115-158 158-200 242-284 326-369	8	A:115-158 B:115-158 A:158-200 B:158-200 A:242-284 B:242-284 A:326-369 B:326-369

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARM_REPEAT	PS50176	Armadillo/plakoglobin ARM repeat profile.	IMA1A_ORYSJ	115-158 158-200 242-284 326-369	4	A:115-158 - A:158-200 - A:242-284 - A:326-369 -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARM_REPEAT	PS50176	Armadillo/plakoglobin ARM repeat profile.	IMA1A_ORYSJ	115-158 158-200 242-284 326-369	4	- B:115-158 - B:158-200 - B:242-284 - B:326-369

(no "Exon" information available for 4BQK)

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:424
 aligned with IMA1A_ORYSJ | Q71VM4 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:424
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490    
          IMA1A_ORYSJ    71 LESLPAMIGGVYSDDNNLQLEATTQFRKLLSIERSPPIEEVIQSGVVPRFVQFLTREDFPQLQFEAAWALTNIASGTSENTKVVIDHGAVPIFVKLLGSSSDDVREQAVWALGNVAGDSPKCRDLVLANGALLPLLAQLNEHTKLSMLRNATWTLSNFCRGKPQPSFEQTRPALPALARLIHSNDEEVLTDACWALSYLSDGTNDKIQAVIEAGVCPRLVELLLHPSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSLLTQNLKKSIKKEACWTISNITAGNKDQIQAVINAGIIGPLVNLLQTAEFDIKKEAAWAISNATSGGSHDQIKYLVSEGCIKPLCDLLICPDIRIVTVCLEGLENILKVGETDKTLAAGDVNVFSQMIDEAEGLEKIENLQSHDNNEIYEKAVKILEAYWM 494
               SCOP domains d4bqka_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------ARM_REPEAT  PDB: A:115-158 UniProt: 115-158 -----------------------------------------------------------------------------------ARM_REPEAT  PDB: A:242-284 UniProt: 242-284-----------------------------------------ARM_REPEAT  PDB: A:326-369 UniProt: 326-369 ----------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------ARM_REPEAT  PDB: A:158-200 UniProt: 158-200------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bqk A  71 GSSLPAMIGGVYSDDNNLQLEATTQFRKLLSIERSPPIEEVIQSGVVPRFVQFLTREDFPQLQFEAAWALTNIASGTSENTKVVIDHGAVPIFVKLLGSSSDDVREQAVWALGNVAGDSPKCRDLVLANGALLPLLAQLNEHTKLSMLRNATWTLSNFCRGKPQPSFEQTRPALPALARLIHSNDEEVLTDACWALSYLSDGTNDKIQAVIEAGVCPRLVELLLHPSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSLLTQNLKKSIKKEACWTISNITAGNKDQIQAVINAGIIGPLVNLLQTAEFDIKKEAAWAISNATSGGSHDQIKYLVSEGCIKPLCDLLICPDIRIVTVCLEGLENILKVGETDKTLAAGDVNVFSQMIDEAEGLEKIENLQSHDNNEIYEKAVKILEAYWM 494
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490

Chain B from PDB  Type:PROTEIN  Length:422
 aligned with IMA1A_ORYSJ | Q71VM4 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:422
                                    82        92       102       112       122       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  
          IMA1A_ORYSJ    73 SLPAMIGGVYSDDNNLQLEATTQFRKLLSIERSPPIEEVIQSGVVPRFVQFLTREDFPQLQFEAAWALTNIASGTSENTKVVIDHGAVPIFVKLLGSSSDDVREQAVWALGNVAGDSPKCRDLVLANGALLPLLAQLNEHTKLSMLRNATWTLSNFCRGKPQPSFEQTRPALPALARLIHSNDEEVLTDACWALSYLSDGTNDKIQAVIEAGVCPRLVELLLHPSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSLLTQNLKKSIKKEACWTISNITAGNKDQIQAVINAGIIGPLVNLLQTAEFDIKKEAAWAISNATSGGSHDQIKYLVSEGCIKPLCDLLICPDIRIVTVCLEGLENILKVGETDKTLAAGDVNVFSQMIDEAEGLEKIENLQSHDNNEIYEKAVKILEAYWM 494
               SCOP domains d4bqkb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------ARM_REPEAT  PDB: B:115-158 UniProt: 115-158 -----------------------------------------------------------------------------------ARM_REPEAT  PDB: B:242-284 UniProt: 242-284-----------------------------------------ARM_REPEAT  PDB: B:326-369 UniProt: 326-369 ----------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------ARM_REPEAT  PDB: B:158-200 UniProt: 158-200------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bqk B  73 SLPAMIGGVYSDDNNLQLEATTQFRKLLSIERSPPIEEVIQSGVVPRFVQFLTREDFPQLQFEAAWALTNIASGTSENTKVVIDHGAVPIFVKLLGSSSDDVREQAVWALGNVAGDSPKCRDLVLANGALLPLLAQLNEHTKLSMLRNATWTLSNFCRGKPQPSFEQTRPALPALARLIHSNDEEVLTDACWALSYLSDGTNDKIQAVIEAGVCPRLVELLLHPSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSLLTQNLKKSIKKEACWTISNITAGNKDQIQAVINAGIIGPLVNLLQTAEFDIKKEAAWAISNATSGGSHDQIKYLVSEGCIKPLCDLLICPDIRIVTVCLEGLENILKVGETDKTLAAGDVNVFSQMIDEAEGLEKIENLQSHDNNEIYEKAVKILEAYWM 494
                                    82        92       102       112       122       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

Chain C from PDB  Type:PROTEIN  Length:12
 aligned with VIRD2_AGRFC | P18592 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:19
                                   425         
          VIRD2_AGRFC   416 SKRPREDDDGEPSERKRER 434
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .....-------....... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 4bqk C 416 SKRPR-------SERKRER 434
                                |    -  |      
                              420     428

Chain D from PDB  Type:PROTEIN  Length:14
 aligned with VIRD2_AGRFC | P18592 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:20
                                   424       434
          VIRD2_AGRFC   415 LSKRPREDDDGEPSERKRER 434
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .......------....... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4bqk D 415 LSKRPRE------SERKRER 434
                                  |  -   |   434
                                421    428

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: alpha-alpha superhelix (690)

Superfamily: ARM repeat (317)

Family: automated matches (39)

Protein domain: automated matches (39)

Rice (Oryza sativa) [TaxId: 4530] (2)

1a	d4bqka_	A:
1b	d4bqkb_	B:

(no "CATH Domain" information available for 4BQK)

(no "Pfam Domain" information available for 4BQK)

Asymmetric Unit(hide GO term definitions)

Chain A,B (IMA1A_ORYSJ | Q71VM4)

molecular function
	GO:0008139	nuclear localization sequence binding	Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus.
	GO:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
	GO:0006607	NLS-bearing protein import into nucleus	The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0006606	protein import into nucleus	The directed movement of a protein from the cytoplasm to the nucleus.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Chain C,D (VIRD2_AGRFC | P18592)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004520	endodeoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0044005	induction by symbiont in host of tumor, nodule, or growth	The process in which an organism causes the formation of a mass of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0051170	nuclear import	The directed movement of substances into the nucleus.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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UniProtKB/Swiss-Prot
	IMA1A_ORYSJ \| Q71VM4	:	2yns 4b8j 4b8o 4b8p 4bpl

4bpl	RICE IMPORTIN_ALPHA IN COMPLEX WITH NUCLEOPLASMIN NLS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (25, 25)

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Related Entries Specified in the PDB File