3D9V - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ROCK I BOUND TO H-1152P A DI-METHYLATED VARIANT OF FASUDIL

Authors :   M. Jacobs

Date :   27 May 08 (Deposition) - 10 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Dimer, Dimerization, Kinase, Phosphorylation, Fasudil, Apoptosis, Atp-Binding, Coiled Coil, Cytoplasm, Golgi Apparatus, Membrane, Metal-Binding, Nucleotide-Binding, Phorbol-Ester Binding, Phosphoprotein, Polymorphism, Serine/Threonine-Protein Kinase, Transferase, Zinc, Zinc- Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Jacobs, K. Hayakawa, L. Swenson, S. Bellon, M. Fleming, P. Taslimi, J. Doran
The Structure Of Dimeric Rock I Reveals The Mechanism For Ligand Selectivity.
J. Biol. Chem. V. 281 260 2006
PubMed-ID: 16249185 | Reference-DOI: 10.1074/JBC.M508847200
(for further references see the PDB file header)

Molecule 1 - RHO-ASSOCIATED PROTEIN KINASE 1
	Chains	:	A, B
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PBEV10
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	N-TERMINAL AND KINASE DOMAIN, RESIDUES 6-415
	Gene	:	ROCK1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RHO-ASSOCIATED, COILED-COIL-CONTAINING PROTEIN KINASE 1, P160 ROCK-1, P160ROCK, RENAL CARCINOMA ANTIGEN NY-REN-35

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	H52	2	Ligand/Ion	(S)-2-METHYL-1-[(4-METHYL-5-ISOQUINOLINE)SULFONYL]-HOMOPIPERAZINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:82 , GLY A:83 , ARG A:84 , ALA A:103 , MET A:153 , GLU A:154 , MET A:156 , ASP A:202 , ASN A:203 , LEU A:205 , PHE A:368	BINDING SITE FOR RESIDUE H52 A 416
2	AC2	SOFTWARE	ILE B:82 , GLY B:83 , ARG B:84 , ALA B:103 , MET B:153 , GLU B:154 , TYR B:155 , MET B:156 , ASP B:202 , ASN B:203 , LEU B:205 , PHE B:368	BINDING SITE FOR RESIDUE H52 B 416

(no "SS Bond" information available for 3D9V)

(no "Cis Peptide Bond" information available for 3D9V)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041055	S	108	N	ROCK1_HUMAN	Polymorphism	55811609	A/B	S	108	N

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	ROCK1_HUMAN	82-105	2	A:82-105 B:82-105
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	ROCK1_HUMAN	194-206	2	A:194-206 B:194-206
3	AGC_KINASE_CTER	PS51285	AGC-kinase C-terminal domain profile.	ROCK1_HUMAN	341-409	2	A:341-405 B:341-402

Asymmetric/Biological Unit (11, 21)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000399799	1	ENSE00001540250	chr18:18691812-18690779	1034	ROCK1_HUMAN	1-31	31	2	A:6-31 B:5-31 (gaps)	26 31
1.2	ENST00000399799	2	ENSE00000666550	chr18:18650574-18650493	82	ROCK1_HUMAN	32-59	28	2	A:32-59 B:32-59	28 28
1.3	ENST00000399799	3	ENSE00000666552	chr18:18629841-18629741	101	ROCK1_HUMAN	59-92	34	2	A:59-92 B:59-92	34 34
1.4	ENST00000399799	4	ENSE00000666554	chr18:18629190-18629053	138	ROCK1_HUMAN	93-138	46	2	A:93-138 B:93-138	46 46
1.5	ENST00000399799	5	ENSE00001106179	chr18:18625428-18625253	176	ROCK1_HUMAN	139-197	59	2	A:139-197 B:139-197	59 59
1.6	ENST00000399799	6	ENSE00001106157	chr18:18624147-18624063	85	ROCK1_HUMAN	197-225	29	2	A:197-225 B:197-225	29 29
1.7	ENST00000399799	7	ENSE00001106151	chr18:18622670-18622526	145	ROCK1_HUMAN	226-274	49	2	A:226-274 B:226-274	49 49
1.8	ENST00000399799	8	ENSE00001106132	chr18:18622196-18622058	139	ROCK1_HUMAN	274-320	47	2	A:274-320 B:274-320	47 47
1.9	ENST00000399799	9	ENSE00001106127	chr18:18619524-18619433	92	ROCK1_HUMAN	320-351	32	2	A:320-351 B:320-351	32 32
1.10	ENST00000399799	10	ENSE00001205106	chr18:18608896-18608737	160	ROCK1_HUMAN	351-404	54	2	A:351-404 B:351-402	54 52
1.11	ENST00000399799	11	ENSE00000666570	chr18:18603641-18603581	61	ROCK1_HUMAN	404-424	21	1	A:404-405 -	2 -
1.12	ENST00000399799	12	ENSE00000666572	chr18:18600200-18600112	89	ROCK1_HUMAN	425-454	30	0	-	-
1.13	ENST00000399799	13	ENSE00000666574	chr18:18595440-18595392	49	ROCK1_HUMAN	454-470	17	0	-	-
1.14	ENST00000399799	14	ENSE00001106120	chr18:18588155-18588020	136	ROCK1_HUMAN	471-516	46	0	-	-
1.15	ENST00000399799	15	ENSE00000666578	chr18:18586751-18586660	92	ROCK1_HUMAN	516-546	31	0	-	-
1.16	ENST00000399799	16	ENSE00000666579	chr18:18586558-18586312	247	ROCK1_HUMAN	547-629	83	0	-	-
1.17	ENST00000399799	17	ENSE00000948798	chr18:18572898-18572792	107	ROCK1_HUMAN	629-664	36	0	-	-
1.18	ENST00000399799	18	ENSE00000948799	chr18:18571287-18571137	151	ROCK1_HUMAN	665-715	51	0	-	-
1.19	ENST00000399799	19	ENSE00000666582	chr18:18567071-18566911	161	ROCK1_HUMAN	715-768	54	0	-	-
1.20	ENST00000399799	20	ENSE00000666583	chr18:18564496-18564312	185	ROCK1_HUMAN	769-830	62	0	-	-
1.21	ENST00000399799	21	ENSE00000666584	chr18:18562793-18562724	70	ROCK1_HUMAN	830-853	24	0	-	-
1.22	ENST00000399799	22	ENSE00000666585	chr18:18559965-18559871	95	ROCK1_HUMAN	854-885	32	0	-	-
1.23	ENST00000399799	23	ENSE00001106143	chr18:18550474-18550309	166	ROCK1_HUMAN	885-940	56	0	-	-
1.24	ENST00000399799	24	ENSE00000948802	chr18:18549169-18549076	94	ROCK1_HUMAN	941-972	32	0	-	-
1.25	ENST00000399799	25	ENSE00000948803	chr18:18548821-18548733	89	ROCK1_HUMAN	972-1001	30	0	-	-
1.26	ENST00000399799	26	ENSE00000948804	chr18:18547901-18547713	189	ROCK1_HUMAN	1002-1064	63	0	-	-
1.27	ENST00000399799	27	ENSE00001133063	chr18:18547037-18546878	160	ROCK1_HUMAN	1065-1118	54	0	-	-
1.28	ENST00000399799	28	ENSE00001133053	chr18:18540167-18540097	71	ROCK1_HUMAN	1118-1141	24	0	-	-
1.29	ENST00000399799	29	ENSE00001106113	chr18:18539889-18539801	89	ROCK1_HUMAN	1142-1171	30	0	-	-
1.30	ENST00000399799	30	ENSE00001659208	chr18:18535206-18535128	79	ROCK1_HUMAN	1171-1197	27	0	-	-
1.31	ENST00000399799	31	ENSE00001592636	chr18:18535005-18534744	262	ROCK1_HUMAN	1198-1285	88	0	-	-
1.32	ENST00000399799	32	ENSE00001652301	chr18:18533746-18533539	208	ROCK1_HUMAN	1285-1354	70	0	-	-
1.33	ENST00000399799	33	ENSE00001540219	chr18:18531348-18529701	1648	ROCK1_HUMAN	1354-1354	1	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:400
 aligned with ROCK1_HUMAN | Q13464 from UniProtKB/Swiss-Prot  Length:1354

    Alignment length:400
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405
          ROCK1_HUMAN     6 SFETRFEKMDNLLRDPKSEVNSDCLLDGLDALVYDLDFPALRKNKNIDNFLSRYKDTINKIRDLRMKAEDYEVVKVIGRGAFGEVQLVRHKSTRKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWARFYTAEVVLALDAIHSMGFIHRDVKPDNMLLDKSGHLKLADFGTCMKMNKEGMVRCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKNSLTFPDDNDISKEAKNLICAFLTDREVRLGRNGVEEIKRHLFFKNDQWAWETLRDTVAPVVPDLSSDIDTSNFDDLEEDKGEEETFPIPKAFVGNQLPFVGFTYYSNRRY 405
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d9vA01 A:6-159,A:359-405 Phosphorylase Kinase; domain 1                                                                                                  3d9vA02 A:160-358 Transferase(Phosphotransferase) domain 1                                                                                                                                             3d9vA01 A:6-159,A:359-405                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhh.....hhhhhhhhhhhh.......eeeeee...eeeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee...........hhhhhh......ee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh...........hhhhhh.........hhhhhhhh.......................................hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER  PDB: A:341-405 UniProt: 341-409                  PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:6-31     Exon 1.2  PDB: A:32-59      ---------------------------------Exon 1.4  PDB: A:93-138 UniProt: 93-138       Exon 1.5  PDB: A:139-197 UniProt: 139-197                  ----------------------------Exon 1.7  PDB: A:226-274 UniProt: 226-274        ----------------------------------------------------------------------------Exon 1.10  PDB: A:351-404 UniProt: 351-404            - Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.3  PDB: A:59-92            --------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:197-225     ------------------------------------------------Exon 1.8  PDB: A:274-320 UniProt: 274-320      -----------------------------------------------------------------------------------1. Transcript 1 (2)
           Transcript 1 (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:320-351        ------------------------------------------------------ Transcript 1 (3)
                 3d9v A   6 SFETRFEKMDNLLRDPKSEVNSDCLLDGLDALVYDLDFPALRKNKNIDNFLSRYKDTINKIRDLRMKAEDYEVVKVIGRGAFGEVQLVRHKSTRKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWARFYTAEVVLALDAIHSMGFIHRDVKPDNMLLDKSGHLKLADFGTCMKMNKEGMVRCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKNSLTFPDDNDISKEAKNLICAFLTDREVRLGRNGVEEIKRHLFFKNDQWAWETLRDTVAPVVPDLSSDIDTSNFDDLEEDKGEEETFPIPKAFVGNQLPFVGFTYYSNRRY 405
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

Chain B from PDB  Type:PROTEIN  Length:398
 aligned with ROCK1_HUMAN | Q13464 from UniProtKB/Swiss-Prot  Length:1354

    Alignment length:402
                                    10        20        30        40        50        60        70        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  
          ROCK1_HUMAN     1 MSTGDSFETRFEKMDNLLRDPKSEVNSDCLLDGLDALVYDLDFPALRKNKNIDNFLSRYKDTINKIRDLRMKAEDYEVVKVIGRGAFGEVQLVRHKSTRKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWARFYTAEVVLALDAIHSMGFIHRDVKPDNMLLDKSGHLKLADFGTCMKMNKEGMVRCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKNSLTFPDDNDISKEAKNLICAFLTDREVRLGRNGVEEIKRHLFFKNDQWAWETLRDTVAPVVPDLSSDIDTSNFDDLEEDKGEEETFPIPKAFVGNQLPFVGFTYYSN 402
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3d    9vB01 B:5-159,B:359-402 Phosphorylase Kinase; domain 1                                                                                                   3d9vB02 B:160-358 Transferase(Phosphotransferase) domain 1                                                                                                                                             3d9vB01 B:5-159,B:359-402                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .h----hhhhhhhhhhhh.......hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhh....hhhhhhhhhhhh.......eeeeee...eeeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee...........hhhhhh......ee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh...........hhhhhh.........hhhhhhhh.......................................hhhhh....... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------N------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER  PDB: B:341-402 UniProt: 341-409               PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:5-31 (gaps)   Exon 1.2  PDB: B:32-59      ---------------------------------Exon 1.4  PDB: B:93-138 UniProt: 93-138       Exon 1.5  PDB: B:139-197 UniProt: 139-197                  ----------------------------Exon 1.7  PDB: B:226-274 UniProt: 226-274        ----------------------------------------------------------------------------Exon 1.10  PDB: B:351-402 UniProt: 351-404           Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.3  PDB: B:59-92            --------------------------------------------------------------------------------------------------------Exon 1.6  PDB: B:197-225     ------------------------------------------------Exon 1.8  PDB: B:274-320 UniProt: 274-320      ---------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:320-351        --------------------------------------------------- Transcript 1 (3)
                 3d9v B   5 MS----FETRFEKMDNLLRDPKSEVNSDCLLDGLDALVYDLDFPALRKNKNIDNFLSRYKDTINKIRDLRMKAEDYEVVKVIGRGAFGEVQLVRHKSTRKVYAMKLLSKFEMIKRSDSAFFWEERDIMAFANSPWVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWARFYTAEVVLALDAIHSMGFIHRDVKPDNMLLDKSGHLKLADFGTCMKMNKEGMVRCDTAVGTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKNSLTFPDDNDISKEAKNLICAFLTDREVRLGRNGVEEIKRHLFFKNDQWAWETLRDTVAPVVPDLSSDIDTSNFDDLEEDKGEEETFPIPKAFVGNQLPFVGFTYYSN 402
                             |    | 10        20        30        40        50        60        70        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  
                             6    7

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 3D9V)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phosphorylase Kinase; domain 1 (1392)

Homologous Superfamily: Phosphorylase Kinase; domain 1 (1392)

Human (Homo sapiens) (1036)

1a	3d9vB01	B:5-159,B:359-402
1b	3d9vA01	A:6-159,A:359-405

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transferase(Phosphotransferase); domain 1 (1379)

Homologous Superfamily: Transferase(Phosphotransferase) domain 1 (1379)

Human (Homo sapiens) (1049)

2a	3d9vA02	A:160-358
2b	3d9vB02	B:160-358

(no "Pfam Domain" information available for 3D9V)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ROCK1_HUMAN | Q13464)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0017049	GTP-Rho binding	Interacting selectively and non-covalently with the GTP-bound form of the Rho protein.
	GO:0017048	Rho GTPase binding	Interacting selectively and non-covalently with Rho protein, any member of the Rho subfamily of the Ras superfamily of monomeric GTPases. Proteins in the Rho subfamily are involved in relaying signals from cell-surface receptors to the actin cytoskeleton.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0007249	I-kappaB kinase/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0007266	Rho protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0003383	apical constriction	The actin-mediated process that results in the contraction of the apical end of a polarized columnar epithelial cell.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0032060	bleb assembly	The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
	GO:0006921	cellular component disassembly involved in execution phase of apoptosis	The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
	GO:0030866	cortical actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of actin-based cytoskeletal structures in the cell cortex, i.e. just beneath the plasma membrane.
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0007159	leukocyte cell-cell adhesion	The attachment of a leukocyte to another cell via adhesion molecules.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0050901	leukocyte tethering or rolling	Transient adhesive interactions between leukocytes and endothelial cells lining blood vessels. Carbohydrates on circulating leukocytes bind selectins on the vessel wall causing the leukocytes to slow down and roll along the inner surface of the vessel wall. During this rolling motion, transitory bonds are formed and broken between selectins and their ligands. Typically the first step in cellular extravasation (the movement of leukocytes out of the circulatory system, towards the site of tissue damage or infection).
	GO:0022614	membrane to membrane docking	The initial attachment of a membrane to a target membrane, mediated by proteins protruding from the two membranes. Docking requires only that the membranes come close enough for the proteins to interact and adhere.
	GO:0051451	myoblast migration	The orderly movement of a myoblast from one site to another, often during the development of a multicellular organism. A myoblast is a cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:1903347	negative regulation of bicellular tight junction assembly	Any process that stops, prevents or reduces the frequency, rate or extent of tight junction assembly.
	GO:0035509	negative regulation of myosin-light-chain-phosphatase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of myosin-light-chain-phosphatase activity.
	GO:0043524	negative regulation of neuron apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
	GO:0032091	negative regulation of protein binding	Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0051894	positive regulation of focal adhesion assembly	Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0032956	regulation of actin cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0032970	regulation of actin filament-based process	Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton.
	GO:0030155	regulation of cell adhesion	Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
	GO:2000145	regulation of cell motility	Any process that modulates the frequency, rate or extent of cell motility.
	GO:0051493	regulation of cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:2000114	regulation of establishment of cell polarity	Any process that modulates the frequency, rate or extent of establishment of cell polarity.
	GO:1903140	regulation of establishment of endothelial barrier	Any process that modulates the frequency, rate or extent of establishment of endothelial barrier.
	GO:0051893	regulation of focal adhesion assembly	Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions.
	GO:0045616	regulation of keratinocyte differentiation	Any process that modulates the frequency, rate or extent of keratinocyte differentiation.
	GO:0051492	regulation of stress fiber assembly	Any process that modulates the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
	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:0006939	smooth muscle contraction	A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length.
	GO:0048010	vascular endothelial growth factor receptor signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
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:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0032059	bleb	A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005814	centriole	A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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(no "Related Entries Specified in the PDB File" available for 3D9V)

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