4DXR - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   HUMAN SUN2-KASH1 COMPLEX

Authors :   B. Sosa, T. U. Schwartz

Date :   28 Feb 12 (Deposition) - 06 Jun 12 (Release) - 06 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.32

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

Keywords :   Beta-Sandwich, Linc Complex, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Sosa, A. Rothballer, U. Kutay, T. U. Schwartz
Linc Complexes Form By Binding Of Three Kash Peptides To Domain Interfaces Of Trimeric Sun Proteins.
Cell(Cambridge, Mass. ) V. 149 1035 2012
PubMed-ID: 22632968 | Reference-DOI: 10.1016/J.CELL.2012.03.046

Molecule 1 - SUN DOMAIN-CONTAINING PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SUN DOMAIN (UNP RESIDUES 522-717)
	Gene	:	SUN2, FRIGG, KIAA0668, RAB5IP, UNC84B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN UNC-84 HOMOLOG B, RAB5-INTERACTING PROTEIN, RAB5IP, SAD1/UNC-84 PROTEIN-LIKE 2

Molecule 2 - NESPRIN-1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 8769-8797
	Gene	:	SYNE1, C6ORF98, KIAA0796, KIAA1262, KIAA1756, MYNE1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ENAPTIN, MYOCYTE NUCLEAR ENVELOPE PROTEIN 1, MYNE-1, NUCLEAR ENVELOPE SPECTRIN REPEAT PROTEIN 1, SYNAPTIC NUCLEAR ENVELOPE PROTEIN 1, SYNE-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	DMU	1	Ligand/Ion	DECYL-BETA-D-MALTOPYRANOSIDE
2	K	1	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	DMU	3	Ligand/Ion	DECYL-BETA-D-MALTOPYRANOSIDE
2	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:552 , LEU A:574 , TRP A:582 , HIS A:584 , GLN A:586 , ARG A:589 , ASN A:600 , HOH A:955 , HOH A:982 , HOH A:1007 , HOH A:1022 , TYR B:8790	BINDING SITE FOR RESIDUE DMU A 801
2	AC2	SOFTWARE	VAL A:590 , GLN A:593 , ASP A:595 , ASN A:600 , TYR A:707	BINDING SITE FOR RESIDUE K A 802

Asymmetric Unit

No.	Residues
1	A:563	-	B:8774
2	A:601	-	A:705

(no "Cis Peptide Bond" information available for 4DXR)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024624	G	671	S	SUN2_HUMAN	Polymorphism	2072797	A	G	671	S

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

Biological Unit 1 (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024624	G	671	S	SUN2_HUMAN	Polymorphism	2072797	A	G	671	S

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUN	PS51469	SUN domain profile.	SUN2_HUMAN	555-716	1	A:555-716

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUN	PS51469	SUN domain profile.	SUN2_HUMAN	555-716	3	A:555-716

(no "Exon" information available for 4DXR)

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:196
 aligned with SUN2_HUMAN | Q9UH99 from UniProtKB/Swiss-Prot  Length:717

    Alignment length:196
                                   531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711      
          SUN2_HUMAN    522 GVTEEQVHHIVKQALQRYSEDRIGLADYALESGGASVISTRCSETYETKTALLSLFGIPLWYHSQSPRVILQPDVHPGNCWAFQGPQGFAVVRLSARIRPTAVTLEHVPKALSPNSTISSAPKDFAIFGFDEDLQQEGTLLGKFTYDQDGEPIQTFHFQAPTMATYQVVELRILTNWGHPEYTCIYRFRVHGEPAH  717
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.........hhhhh.eeee...........eeeee..eeeeee..hhhhhhh........eeee...eeeeeeeeeeeeeeeeeee..hhhhhhhhh......eeeeeee........eeeeeee.......eeeee........eeeeeeee........eeee.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------SUN  PDB: A:555-716 UniProt: 555-716                                                                                                                              - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dxr A  522 GVTEEQVHHIVKQALQRYSEDRIGLADYALESGGASVISTRCSETYETKTALLSLFGIPLWYHSQSPRVILQPDVHPGNCWAFQGPQGFAVVRLSARIRPTAVTLEHVPKALSPNSTISSAPKDFAIFGFDEDLQQEGTLLGKFTYDQDGEPIQTFHFQAPTMATYQVVELRILTNWGHPEYTCIYRFRVHGEPAH  717
                                   531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711

Chain B from PDB  Type:PROTEIN  Length:25
 aligned with SYNE1_HUMAN | Q8NF91 from UniProtKB/Swiss-Prot  Length:8797

    Alignment length:25
                                  8782      8792     
         SYNE1_HUMAN   8773 SCALSNNFARSFHPMLRYTNGPPPL 8797
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..............eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                4dxr B 8773 SCALSNNFARSFHPMLRYTNGPPPL 8797
                                  8782      8792

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 '\|'

(no "SCOP Domain" information available for 4DXR)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (SUN2_HUMAN | Q9UH99)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005521	lamin binding	Interacting selectively and non-covalently with lamin; any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	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:0051642	centrosome localization	Any process in which a centrosome is transported to, and/or maintained in, a specific location within the cell.
	GO:0090286	cytoskeletal anchoring at nuclear membrane	The process in which cytoskeletal filaments are directly or indirectly linked to the nuclear membrane.
	GO:0007052	mitotic spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
	GO:0006998	nuclear envelope organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
	GO:0090292	nuclear matrix anchoring at nuclear membrane	The process in which the nuclear matrix, the dense fibrillar network lying on the inner side of the nuclear membrane, is directly or indirectly linked to the nuclear membrane.
	GO:0007097	nuclear migration	The directed movement of the nucleus.
	GO:0031022	nuclear migration along microfilament	The directed movement of the nucleus along microfilaments within the cell, mediated by motor proteins.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
cellular component
	GO:0034993	LINC complex	A protein complex that spans the nuclear outer and inner membranes, thereby linking the major cytoplasmic cytoskeleton elements to the nuclear lumen; the complex is conserved in eukaryotes and contains proteins with SUN and KASH domains.
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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:0005639	integral component of nuclear inner membrane	The component of the nuclear inner 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.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	GO:0005637	nuclear inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	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.

Chain B (SYNE1_HUMAN | Q8NF91)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005521	lamin binding	Interacting selectively and non-covalently with lamin; any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0007030	Golgi organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
	GO:0090286	cytoskeletal anchoring at nuclear membrane	The process in which cytoskeletal filaments are directly or indirectly linked to the nuclear membrane.
	GO:0040023	establishment of nucleus localization	The directed movement of the nucleus to a specific location within a cell.
	GO:0042692	muscle cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a muscle cell.
	GO:0090292	nuclear matrix anchoring at nuclear membrane	The process in which the nuclear matrix, the dense fibrillar network lying on the inner side of the nuclear membrane, is directly or indirectly linked to the nuclear membrane.
	GO:0006997	nucleus organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0034993	LINC complex	A protein complex that spans the nuclear outer and inner membranes, thereby linking the major cytoplasmic cytoskeleton elements to the nuclear lumen; the complex is conserved in eukaryotes and contains proteins with SUN and KASH domains.
	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: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.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005640	nuclear outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
	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:0045211	postsynaptic membrane	A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
	GO:0030017	sarcomere	The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.

Asymmetric Unit
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	4dxr
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	SUN2_HUMAN \| Q9UH99	:	3unp 4dxs 4dxt 4fi9

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