2XN4 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE KELCH DOMAIN OF HUMAN KLHL2 (MAYVEN)

Authors :   P. Canning, V. Hozjan, C. D. O. Cooper, V. Ayinampudi, M. Vollmar, A. C. W F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, C. Bountra, A. N. Bullock

Date :   30 Jul 10 (Deposition) - 18 Aug 10 (Release) - 27 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.99

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

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

Reference :   P. Canning, C. D. O. Cooper, T. Krojer, J. W. Murray, A. C. W. Pike, A. Chaikuad, T. Keates, C. Thangaratnarajah, V. Hojzan, B. D. Marsden O. Gileadi, S. Knapp, F. Von Delft, A. N. Bullock
Structural Basis For Cul3 Assembly With The Btb-Kelch Family Of E3 Ubiquitin Ligases.
J. Biol. Chem. V. 288 7803 2013
PubMed-ID: 23349464 | Reference-DOI: 10.1074/JBC.M112.437996

Molecule 1 - KELCH-LIKE PROTEIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Expression System Vector Type	:	PLASMID
	Fragment	:	KELCH DOMAIN, RESIDUES 294-591
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	MAMMALIAN GENE COLLECTION (MGC)
	Synonym	:	ACTIN-BINDING PROTEIN MAYVEN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	NA	2	Ligand/Ion	SODIUM ION
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	NA	-1	Ligand/Ion	SODIUM ION
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	NA	-1	Ligand/Ion	SODIUM ION
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:345 , ARG A:366 , SER A:391	BINDING SITE FOR RESIDUE NA A 900
02	AC2	SOFTWARE	ARG A:510 , LYS A:511 , SER A:512 , HOH A:2257 , HOH A:2258 , HOH A:2259	BINDING SITE FOR RESIDUE SO4 A 901
03	AC3	SOFTWARE	ARG A:321 , ARG A:342 , HOH A:2260 , HOH A:2261 , HOH A:2262 , ARG B:387	BINDING SITE FOR RESIDUE SO4 A 902
04	AC4	SOFTWARE	SER A:415 , ARG A:436 , HOH A:2077 , HOH A:2263 , HOH A:2264 , SER B:341 , ASN B:362 , VAL B:367 , THR B:369 , HOH B:2027	BINDING SITE FOR RESIDUE SO4 A 903
05	AC5	SOFTWARE	GLY A:363 , SER A:364 , HIS B:429 , ALA B:431 , ASN B:474	BINDING SITE FOR RESIDUE EDO A 904
06	AC6	SOFTWARE	ARG B:345 , ARG B:366 , SER B:391	BINDING SITE FOR RESIDUE NA B 900
07	AC7	SOFTWARE	ARG B:510 , LYS B:511 , SER B:512 , HOH B:2267 , HOH B:2268	BINDING SITE FOR RESIDUE SO4 B 901
08	AC8	SOFTWARE	SER A:341 , ASN A:362 , VAL A:367 , THR A:369 , HOH A:2016 , SER B:415 , ARG B:436 , HOH B:2085 , HOH B:2269 , HOH B:2270	BINDING SITE FOR RESIDUE SO4 B 902
09	AC9	SOFTWARE	ARG A:387 , ARG B:321 , ARG B:342 , HOH B:2007 , HOH B:2271 , HOH B:2272	BINDING SITE FOR RESIDUE SO4 B 903
10	BC1	SOFTWARE	HIS A:429 , ASN A:474 , GLY B:363 , SER B:364 , HOH B:2036 , HOH B:2273	BINDING SITE FOR RESIDUE EDO B 904

(no "SS Bond" information available for 2XN4)

Asymmetric Unit

No.	Residues
1	Ala A:316	-	Pro A:317
2	Ala B:316	-	Pro B:317

(no "SAP(SNP)/Variant" information available for 2XN4)

(no "PROSITE Motif" information available for 2XN4)

(no "Exon" information available for 2XN4)

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:286
 aligned with KLHL2_HUMAN | O95198 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:286
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585      
          KLHL2_HUMAN   306 PKLMVVVGGQAPKAIRSVECYDFKEERWHQVAELPSRRCRAGMVYMAGLVFAVGGFNGSLRVRTVDSYDPVKDQWTSVANMRDRRSTLGAAVLNGLLYAVGGFDGSTGLSSVEAYNIKSNEWFHVAPMNTRRSSVGVGVVGGLLYAVGGYDGASRQCLSTVECYNATTNEWTYIAEMSTRRSGAGVGVLNNLLYAVGGHDGPLVRKSVEVYDPTTNAWRQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPTTDKWTVVSSCMSTGRSYAGVTVIDK 591
               SCOP domains d2xn4a_ A: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2xn4A00 A:306-591 Kelch-like ech-associated protein 1                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..........eeeee....eeeee..........eeeee..eeeee...........eeeee....eeeee..........eeeee..eeeeeeee....eeeeeeeee....eeeee..........eeeee..eeeee..ee....ee...eeeee....eeeee..........eeeee..eeeee...........eeeee....eeeee..........eeeee..eeeee...........eeee......eee............eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xn4 A 306 PKLMVVVGGQAPKAIRSVECYDFKEERWHQVAELPSRRCRAGMVYMAGLVFAVGGFNGSLRVRTVDSYDPVKDQWTSVANMRDRRSTLGAAVLNGLLYAVGGFDGSTGLSSVEAYNIKSNEWFHVAPMNTRRSSVGVGVVGGLLYAVGGYDVASRQCLSTVECYNATTNEWTYIAEMSTRRSGAGVGVLNNLLYAVGGHDGPLVRKSVEVYDPTTNAWRQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPTTDKWTVVSSCMSTGRSYAGVTVIDK 591
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with KLHL2_HUMAN | O95198 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:286
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585      
          KLHL2_HUMAN   306 PKLMVVVGGQAPKAIRSVECYDFKEERWHQVAELPSRRCRAGMVYMAGLVFAVGGFNGSLRVRTVDSYDPVKDQWTSVANMRDRRSTLGAAVLNGLLYAVGGFDGSTGLSSVEAYNIKSNEWFHVAPMNTRRSSVGVGVVGGLLYAVGGYDGASRQCLSTVECYNATTNEWTYIAEMSTRRSGAGVGVLNNLLYAVGGHDGPLVRKSVEVYDPTTNAWRQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPTTDKWTVVSSCMSTGRSYAGVTVIDK 591
               SCOP domains d2xn4b_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2xn4B00 B:306-591 Kelch-like ech-associated protein 1                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B01 B:532-577                     -------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B02 B:532-577                     -------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B03 B:532-577                     -------------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B04 B:532-577                     -------------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B05 B:532-577                     -------------- Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B06 B:532-577                     -------------- Pfam domains (6)
           Pfam domains (7) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B07 B:532-577                     -------------- Pfam domains (7)
           Pfam domains (8) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B08 B:532-577                     -------------- Pfam domains (8)
           Pfam domains (9) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B09 B:532-577                     -------------- Pfam domains (9)
          Pfam domains (10) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B10 B:532-577                     -------------- Pfam domains (10)
          Pfam domains (11) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B11 B:532-577                     -------------- Pfam domains (11)
          Pfam domains (12) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kelch_1-2xn4B12 B:532-577                     -------------- Pfam domains (12)
         Sec.struct. author .eeeeee..........eeeee....eeeee..........eeeee..eeeee...........eeeee....eeeee..........eeeee..eeeee...........eeeee....eeeee..........eeeee..eeeee..ee....ee...eeeee....eeee...........eeeee..eeeee...........eeeee....eeeee..........eeeee..eeeee...........eeee......eee............eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xn4 B 306 PKLMVVVGGQAPKAIRSVECYDFKEERWHQVAELPSRRCRAGMVYMAGLVFAVGGFNGSLRVRTVDSYDPVKDQWTSVANMRDRRSTLGAAVLNGLLYAVGGFDGSTGLSSVEAYNIKSNEWFHVAPMNTRRSSVGVGVVGGLLYAVGGYDVASRQCLSTVECYNATTNEWTYIAEMSTRRSGAGVGVLNNLLYAVGGHDGPLVRKSVEVYDPTTNAWRQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPTTDKWTVVSSCMSTGRSYAGVTVIDK 591
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585

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 beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: Kelch motif (18)

Family: automated matches (4)

Protein domain: automated matches (4)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d2xn4a_	A:
1b	d2xn4b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 6 Propellor (215)

Topology: Neuraminidase (215)

Homologous Superfamily: Kelch-like ech-associated protein 1 (10)

Human (Homo sapiens) (5)

1a	2xn4A00	A:306-591
1b	2xn4B00	B:306-591

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta_propeller (192)

Family: Kelch_1 (10)

Homo sapiens (Human) (4)

1a	Kelch_1-2xn4B01	B:532-577
1b	Kelch_1-2xn4B02	B:532-577
1c	Kelch_1-2xn4B03	B:532-577
1d	Kelch_1-2xn4B04	B:532-577
1e	Kelch_1-2xn4B05	B:532-577
1f	Kelch_1-2xn4B06	B:532-577
1g	Kelch_1-2xn4B07	B:532-577
1h	Kelch_1-2xn4B08	B:532-577
1i	Kelch_1-2xn4B09	B:532-577
1j	Kelch_1-2xn4B10	B:532-577
1k	Kelch_1-2xn4B11	B:532-577
1l	Kelch_1-2xn4B12	B:532-577

Asymmetric Unit(hide GO term definitions)

Chain A,B (KLHL2_HUMAN | O95198)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	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:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	GO:0031463	Cul3-RING ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul3 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a BTB-domain-containing protein.
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030027	lamellipodium	A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:316 - Pro A:317	[ RasMol ]
		Ala B:316 - Pro B:317	[ RasMol ]

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	2xn4
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(no "Related Entries Specified in the PDB File" available for 2XN4)

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