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Asym./Biol. Unit (Jmol Viewer)

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Title :   CO-CRYSTAL STRUCTURE OF RAP1 IN COMPLEX WITH KRIT1

Authors :   X. Li, R. Zhang, T. J. Boggon

Date :   27 Feb 12 (Deposition) - 16 May 12 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Gtpase, Ferm, Protein-Protein Interaction, Gtp Binding, Cytoplasmic, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Li, R. Zhang, K. M. Draheim, W. Liu, D. A. Calderwood, T. J. Boggon
Structural Basis For Small G Protein Effector Interaction O Ras-Related Protein 1 (Rap1) And Adaptor Protein Krev Interaction Trapped 1 (Krit1).
J. Biol. Chem. V. 287 22317 2012
PubMed-ID: 22577140 | Reference-DOI: 10.1074/JBC.M112.361295

Molecule 1 - RAS-RELATED PROTEIN RAP-1B
	Chains	:	A
	EC Number	:	3.6.5.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET-32
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	OK/SW-CL.11, RAP1B, RAS-RELATED PROTEIN RAP-1B (RAP1B)
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GTP-BINDING PROTEIN SMG P21B

Molecule 2 - KREV INTERACTION TRAPPED PROTEIN 1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX 6P-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	FERM DOMAIN
	Gene	:	CCM1, KREV INTERACTION TRAPPED PROTEIN 1 (KRIT1), KRIT1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	KREV INTERACTION TRAPPED 1, CEREBRAL CAVERNOUS MALFORMATIONS 1 PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GSP	1	Ligand/Ion	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:12 , GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , GLU A:30 , TYR A:32 , THR A:35 , GLY A:60 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:147 , ALA A:148 , LYS A:149 , MG A:202 , HOH A:316 , HOH A:354 , HOH A:374 , HOH A:382 , HOH A:386	BINDING SITE FOR RESIDUE GSP A 201
2	AC2	SOFTWARE	SER A:17 , THR A:35 , GSP A:201 , HOH A:381 , HOH A:382	BINDING SITE FOR RESIDUE MG A 202

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

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

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023574	K	569	E	KRIT1_HUMAN	Disease (CCM1)	---	B	K	569	E

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAS	PS51421	small GTPase Ras family profile.	RAP1B_HUMAN	1-184	1	A:1-167
2	FERM_3	PS50057	FERM domain profile.	KRIT1_HUMAN	420-734	1	B:420-729

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1e	ENST00000393436	1e	ENSE00001817232	chr12:69004688-69004832	145	RAP1B_HUMAN	-	0	0	-	-
1.3	ENST00000393436	3	ENSE00002170663	chr12:69042479-69042561	83	RAP1B_HUMAN	1-19	19	1	A:1-19	19
1.4a	ENST00000393436	4a	ENSE00001621515	chr12:69044180-69044248	69	RAP1B_HUMAN	20-42	23	1	A:20-42	23
1.5a	ENST00000393436	5a	ENSE00001207248	chr12:69045775-69045831	57	RAP1B_HUMAN	43-61	19	1	A:43-61	19
1.6	ENST00000393436	6	ENSE00001673144	chr12:69047892-69048032	141	RAP1B_HUMAN	62-108	47	1	A:62-108	47
1.7a	ENST00000393436	7a	ENSE00001755393	chr12:69050086-69050229	144	RAP1B_HUMAN	109-156	48	1	A:109-156	48
1.8	ENST00000393436	8	ENSE00001207265	chr12:69050881-69050997	117	RAP1B_HUMAN	157-184	28	1	A:157-167	11
1.9b	ENST00000393436	9b	ENSE00001937531	chr12:69053060-69054287	1228	RAP1B_HUMAN	-	0	0	-	-

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:168
 aligned with RAP1B_HUMAN | P61224 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
          RAP1B_HUMAN     - -MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR 167
               SCOP domains d4dxaa_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -RAS  PDB: A:1-167 UniProt: 1-184                                                                                                                                        PROSITE
               Transcript 1 -Exon 1.3           Exon 1.4a  PDB: A:20-42Exon 1.5a          Exon 1.6  PDB: A:62-108 UniProt: 62-108        Exon 1.7a  PDB: A:109-156 UniProt: 109-156      Exon 1.8    Transcript 1
                 4dxa A   0 SMREYKLVVLGSVGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR 167
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159

Chain B from PDB  Type:PROTEIN  Length:302
 aligned with KRIT1_HUMAN | O00522 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:311
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728 
          KRIT1_HUMAN   419 YEKVRIYRMDGSYRSVELKHGNNTTVQQIMEGMRLSQETQQYFTIWICSENLSLQLKPYHKPLQHVRDWPEILAELTNLDPQRETPQLFLRRDVRLPLEVEKQIEDPLAILILFDEARYNLLKGFYTAPDAKLITLASLLLQIVYGNYESKKHKQGFLNEENLKSIVPVTKLKSKAPHWTNRILHEYKNLSTSEGVSKEMHHLQRMFLQNCWEIPTYGAAFFTGQIFTKASPSNHKVIPVYVGVNIKGLHLLNMETKALLISLKYGCFMWQLGDTDTCFQIHSMENKMSFIVHTKQAGLVVKLLMKLNGQL 729
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeee..hhhhhhhhhhhh......hhhh.eeeeee....eee.....hhhhhhhhhhhhhhhhh.........eeeeee....hhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhh..........hhhhhhhhhhhhhhhhhh--....hhhhhhhhhhhhhhh......eeeeeee..-------..eeeeeee...eeeeee.....eeeeee...eeeee.....eeeeee.....eeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------E---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -FERM_3  PDB: B:420-729 UniProt: 420-734                                                                                                                                                                                                                                                                                PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxa B 419 FEKVRIYRMDGSYRSVELKHGNNTTVQQIMEGMRLSQETQQYFTIWICSENLSLQLKPYHKPLQHVRDWPEILAELTNLDPQRETPQLFLRRDVRLPLEVEKQIEDPLAILILFDEARYNLLKGFYTAPDAKLITLASLLLQIVYGNYESKKHKQGFLNEENLKSIVPVTKLKSKAPHWTNRILHEYKNLST--GVSKEMHHLQRMFLQNCWEIPTYGAAFFTGQIFT-------KVIPVYVGVNIKGLHLLNMETKALLISLKYGCFMWQLGDTDTCFQIHSMENKMSFIVHTKQAGLVVKLLMKLNGQL 729
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608 |  |  618       628       638       | -     | 658       668       678       688       698       708       718       728 
                                                                                                                                                                                                                         610  |                              646     654                                                                           
                                                                                                                                                                                                                            613

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: automated matches (173)

Human (Homo sapiens) [TaxId: 9606] (112)

d4dxaa_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RAP1B_HUMAN | P61224)

molecular function
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0032486	Rap protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rap family of proteins switching to a GTP-bound active state.
	GO:0071320	cellular response to cAMP	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0061028	establishment of endothelial barrier	The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
	GO:0030033	microvillus assembly	Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.
	GO:1901888	regulation of cell junction assembly	Any process that modulates the frequency, rate or extent of cell junction assembly.
	GO:2000114	regulation of establishment of cell polarity	Any process that modulates the frequency, rate or extent of establishment of cell polarity.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.
	GO:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B (KRIT1_HUMAN | O00522)

molecular function
	GO:0030695	GTPase regulator activity	Modulates the rate of GTP hydrolysis by a GTPase.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	GO:0005546	phosphatidylinositol-4,5-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:2000352	negative regulation of endothelial cell apoptotic process	Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
	GO:0010596	negative regulation of endothelial cell migration	Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0001937	negative regulation of endothelial cell proliferation	Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
	GO:0032092	positive regulation of protein binding	Any process that activates or increases the frequency, rate or extent of protein binding.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:2000114	regulation of establishment of cell polarity	Any process that modulates the frequency, rate or extent of establishment of cell polarity.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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(no "Related Entries Specified in the PDB File" available for 4DXA)

Description

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Ligands, Modified Residues, Ions (2, 2)

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