3BRW - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF THE RAP-RAPGAP COMPLEX

Authors :   A. Scrima, C. Thomas, D. Deaconescu, A. Wittinghofer

Date :   21 Dec 07 (Deposition) - 11 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Gap, G Proteins, Gtpase, Rap, Gtpase Activation, Gtp- Binding, Gtp Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Scrima, C. Thomas, D. Deaconescu, A. Wittinghofer
The Rap-Rapgap Complex: Gtp Hydrolysis Without Catalytic Glutamine And Arginine Residues
Embo J. V. 27 1145 2008
PubMed-ID: 18309292 | Reference-DOI: 10.1038/EMBOJ.2008.30
(for further references see the PDB file header)

Molecule 1 - RAP1 GTPASE-ACTIVATING PROTEIN 1
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX4T1
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RAP1GAP, UNP RESIDUES 75-415
	Gene	:	RAP1GAP
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RAP1GAP1, RAP1GAP

Molecule 2 - RAS-RELATED PROTEIN RAP-1B
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PTAC
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-167
	Gene	:	RAP1B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GTP-BINDING PROTEIN SMG P21B

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	BEF	1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	BEF	-1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
2	GDP	-1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	BEF	-1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
2	GDP	-1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	BEF	-1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
2	GDP	-1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	BEF	1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER D:17 , THR D:35 , HOH D:174 , HOH D:175	BINDING SITE FOR RESIDUE MG D 172
2	AC2	SOFTWARE	ASN B:290 , GLY D:12 , GLY D:13 , LYS D:16 , TYR D:32 , PRO D:34 , THR D:35 , GLY D:60 , HOH D:175	BINDING SITE FOR RESIDUE BEF D 170
3	AC3	SOFTWARE	GLN B:280 , GLY D:13 , GLY D:15 , LYS D:16 , SER D:17 , ALA D:18 , GLU D:30 , LYS D:31 , TYR D:32 , ASN D:116 , LYS D:117 , ASP D:119 , LEU D:120 , SER D:147 , ALA D:148 , LYS D:149 , HOH D:174 , HOH D:175	BINDING SITE FOR RESIDUE GDP D 171

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

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

Asymmetric Unit (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047792	A	107	T	RPGP1_HUMAN	Polymorphism	2275363	A/B/C	T	107	T
2	UniProt	VAR_035547	C	257	R	RPGP1_HUMAN	Unclassified	---	A/B/C	C	257	R

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047792	A	107	T	RPGP1_HUMAN	Polymorphism	2275363	A	T	107	T
2	UniProt	VAR_035547	C	257	R	RPGP1_HUMAN	Unclassified	---	A	C	257	R

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047792	A	107	T	RPGP1_HUMAN	Polymorphism	2275363	B	T	107	T
2	UniProt	VAR_035547	C	257	R	RPGP1_HUMAN	Unclassified	---	B	C	257	R

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

Biological Unit 3 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047792	A	107	T	RPGP1_HUMAN	Polymorphism	2275363	C	T	107	T
2	UniProt	VAR_035547	C	257	R	RPGP1_HUMAN	Unclassified	---	C	C	257	R

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

Biological Unit 4 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAS	PS51421	small GTPase Ras family profile.	RAP1B_HUMAN	1-184	1	D:1-167
2	RAPGAP	PS50085	Rap GTPase activating proteins domain profile.	RPGP1_HUMAN	181-397	3	A:181-397 B:181-397 C:181-397

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAS	PS51421	small GTPase Ras family profile.	RAP1B_HUMAN	1-184	0	-
2	RAPGAP	PS50085	Rap GTPase activating proteins domain profile.	RPGP1_HUMAN	181-397	1	A:181-397 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAS	PS51421	small GTPase Ras family profile.	RAP1B_HUMAN	1-184	0	-
2	RAPGAP	PS50085	Rap GTPase activating proteins domain profile.	RPGP1_HUMAN	181-397	1	- B:181-397 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAS	PS51421	small GTPase Ras family profile.	RAP1B_HUMAN	1-184	0	-
2	RAPGAP	PS50085	Rap GTPase activating proteins domain profile.	RPGP1_HUMAN	181-397	1	- - C:181-397

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAS	PS51421	small GTPase Ras family profile.	RAP1B_HUMAN	1-184	1	D:1-167
2	RAPGAP	PS50085	Rap GTPase activating proteins domain profile.	RPGP1_HUMAN	181-397	0	- - -

Asymmetric Unit (17, 39)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000374765	1d	ENSE00001922447	chr1:21995799-21995747	53	RPGP1_HUMAN	-	0	0	-	-
1.7	ENST00000374765	7	ENSE00001771682	chr1:21976289-21976254	36	RPGP1_HUMAN	-	0	0	-	-
1.9	ENST00000374765	9	ENSE00001693140	chr1:21952890-21952797	94	RPGP1_HUMAN	-	0	0	-	-
1.12b	ENST00000374765	12b	ENSE00002162403	chr1:21946543-21946508	36	RPGP1_HUMAN	1-6	6	0	-	-
1.13	ENST00000374765	13	ENSE00001042663	chr1:21945565-21945518	48	RPGP1_HUMAN	7-22	16	0	-	-
1.14a	ENST00000374765	14a	ENSE00001277338	chr1:21944465-21944427	39	RPGP1_HUMAN	23-35	13	0	-	-
1.15b	ENST00000374765	15b	ENSE00001042624	chr1:21943984-21943799	186	RPGP1_HUMAN	36-97	62	3	A:76-97 B:78-97 C:78-97	22 20 20
1.16	ENST00000374765	16	ENSE00001042672	chr1:21940582-21940479	104	RPGP1_HUMAN	98-132	35	3	A:98-132 B:98-132 C:98-132	35 35 35
1.17	ENST00000374765	17	ENSE00001210991	chr1:21940199-21940121	79	RPGP1_HUMAN	132-158	27	3	A:132-158 B:132-158 C:132-158	27 27 27
1.18a	ENST00000374765	18a	ENSE00001042668	chr1:21939722-21939669	54	RPGP1_HUMAN	159-176	18	3	A:159-176 B:159-176 C:159-176	18 18 18
1.19	ENST00000374765	19	ENSE00002197342	chr1:21938602-21938519	84	RPGP1_HUMAN	177-204	28	3	A:177-204 B:177-204 C:177-204	28 28 28
1.20a	ENST00000374765	20a	ENSE00001754897	chr1:21938309-21938209	101	RPGP1_HUMAN	205-238	34	3	A:205-238 B:205-238 C:205-238	34 34 34
1.21b	ENST00000374765	21b	ENSE00001650448	chr1:21938074-21937945	130	RPGP1_HUMAN	238-281	44	3	A:238-281 B:238-281 C:238-281	44 44 44
1.22b	ENST00000374765	22b	ENSE00001634331	chr1:21936768-21936613	156	RPGP1_HUMAN	282-333	52	3	A:282-333 B:282-333 C:282-333 (gaps)	52 52 52
1.23a	ENST00000374765	23a	ENSE00001758731	chr1:21936139-21936068	72	RPGP1_HUMAN	334-357	24	3	A:334-357 B:334-357 C:334-357	24 24 24
1.23c	ENST00000374765	23c	ENSE00001653678	chr1:21935429-21935343	87	RPGP1_HUMAN	358-386	29	3	A:358-386 B:358-386 C:358-386	29 29 29
1.24a	ENST00000374765	24a	ENSE00001699035	chr1:21934843-21934706	138	RPGP1_HUMAN	387-432	46	3	A:387-411 B:387-414 C:387-413	25 28 27
1.25	ENST00000374765	25	ENSE00001770247	chr1:21932690-21932559	132	RPGP1_HUMAN	433-476	44	0	-	-
1.26f	ENST00000374765	26f	ENSE00001732229	chr1:21929406-21929297	110	RPGP1_HUMAN	477-513	37	0	-	-
1.27	ENST00000374765	27	ENSE00001751806	chr1:21928290-21928177	114	RPGP1_HUMAN	513-551	39	0	-	-
1.28b	ENST00000374765	28b	ENSE00001715476	chr1:21926110-21925987	124	RPGP1_HUMAN	551-592	42	0	-	-
1.29a	ENST00000374765	29a	ENSE00001662261	chr1:21924995-21924893	103	RPGP1_HUMAN	593-627	35	0	-	-
1.30b	ENST00000374765	30b	ENSE00001765225	chr1:21924557-21924454	104	RPGP1_HUMAN	627-661	35	0	-	-
1.31	ENST00000374765	31	ENSE00001769818	chr1:21924221-21924179	43	RPGP1_HUMAN	662-663	2	0	-	-
1.32b	ENST00000374765	32b	ENSE00001924180	chr1:21923757-21922714	1044	RPGP1_HUMAN	-	0	0	-	-

2.1e	ENST00000393436	1e	ENSE00001817232	chr12:69004688-69004832	145	RAP1B_HUMAN	-	0	0	-	-
2.3	ENST00000393436	3	ENSE00002170663	chr12:69042479-69042561	83	RAP1B_HUMAN	1-19	19	1	D:1-19	19
2.4a	ENST00000393436	4a	ENSE00001621515	chr12:69044180-69044248	69	RAP1B_HUMAN	20-42	23	1	D:20-42	23
2.5a	ENST00000393436	5a	ENSE00001207248	chr12:69045775-69045831	57	RAP1B_HUMAN	43-61	19	1	D:43-61	19
2.6	ENST00000393436	6	ENSE00001673144	chr12:69047892-69048032	141	RAP1B_HUMAN	62-108	47	1	D:62-108	47
2.7a	ENST00000393436	7a	ENSE00001755393	chr12:69050086-69050229	144	RAP1B_HUMAN	109-156	48	1	D:109-156	48
2.8	ENST00000393436	8	ENSE00001207265	chr12:69050881-69050997	117	RAP1B_HUMAN	157-184	28	1	D:157-167	11
2.9b	ENST00000393436	9b	ENSE00001937531	chr12:69053060-69054287	1228	RAP1B_HUMAN	-	0	0	-	-

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:336
 aligned with RPGP1_HUMAN | P47736 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:336
                                    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      
          RPGP1_HUMAN    76 TTKVKLECNPTARIYRKHFLGKEHFNYYSLDAALGHLVFSLKYDVIGDQEHLRLLLRTKCRTYHDVIPISCLTEFPNVVQMAKLVCEDVNVDRFYPVLYPKASRLIVTFDEHVISNNFKFGVIYQKLGQTSEEELFSTNEESPAFVEFLEFLGQKVKLQDFKGFRGGLDVTHGQTGTESVYCNFRNKEIMFHVSTKLPYTEGDAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASNFLHAYVVVQAEGGGPDGPLYKVSVTARDDVPFFGPPLPDPAVFRKGPEFQEFLLTKLINAEYACYKAEKFAKLEERTRAALLETLYEELHIHSQSMMGL 411
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhh.....eeeeeee...eeeeeeeeeeee..eeeeeeeee....eeeeeee........hhhhhhhh..........ee....hhhhhhhhhhh.....eeeeeeeee......hhhhhh....hhhhhhhhhhhheeee.hhh................eeeeee....eeeeee............hhhhhhhhh...eeeeee.................eeeeee...........eeeee....................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------T-----------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------RAPGAP  PDB: A:181-397 UniProt: 181-397                                                                                                                                                                                  -------------- PROSITE (2)
           Transcript 1 (1) Exon 1.15b            Exon 1.16  PDB: A:98-132           --------------------------Exon 1.18a        Exon 1.19  PDB: A:177-204   Exon 1.20a  PDB: A:205-238        -------------------------------------------Exon 1.22b  PDB: A:282-333 UniProt: 282-333         Exon 1.23a              Exon 1.23c  PDB: A:358-386   Exon 1.24a  PDB: A:387-41 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.17  PDB: A:132-158  -------------------------------------------------------------------------------Exon 1.21b  PDB: A:238-281 UniProt: 238-281 ---------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3brw A  76 TTKVKLECNPTARIYRKHFLGKEHFNYYSLDTALGHLVFSLKYDVIGDQEHLRLLLRTKCRTYHDVIPISCLTEFPNVVQMAKLVCEDVNVDRFYPVLYPKASRLIVTFDEHVISNNFKFGVIYQKLGATSEEELFSTNEESPAFVEFLEFLGQKVKLQDFKGFRGGLDVTHGQTGTESVYCNFRNKEIMFHVSTKLPYTEGDAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASNFLHAYVVVQAEGGGPDGPLYKVSVTARDDVPFFGPPLPDPAVFRKGPEFQEFLLTKLINAEYACYKAEKFAKLEERTRAALLETLYEELHIHSQSMMGL 411
                                    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:337
 aligned with RPGP1_HUMAN | P47736 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:337
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       
          RPGP1_HUMAN    78 KVKLECNPTARIYRKHFLGKEHFNYYSLDAALGHLVFSLKYDVIGDQEHLRLLLRTKCRTYHDVIPISCLTEFPNVVQMAKLVCEDVNVDRFYPVLYPKASRLIVTFDEHVISNNFKFGVIYQKLGQTSEEELFSTNEESPAFVEFLEFLGQKVKLQDFKGFRGGLDVTHGQTGTESVYCNFRNKEIMFHVSTKLPYTEGDAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASNFLHAYVVVQAEGGGPDGPLYKVSVTARDDVPFFGPPLPDPAVFRKGPEFQEFLLTKLINAEYACYKAEKFAKLEERTRAALLETLYEELHIHSQSMMGLGGD 414
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.....eeeeeee...eeeeeeeeeeee..eeeeeeeee....eeee...........hhhhhhhhhh........ee....hhhhhhhhhhh.....eeeeeeeee.....hhhhhhh......hhhhhhhhhheeee....................eeeee.....eeeeee............hhhhhhhhh...eeeeee......hhhhh......eeeeee.........eeeeeeee...............eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -----------------------------T-----------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------RAPGAP  PDB: B:181-397 UniProt: 181-397                                                                                                                                                                                  ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.15b          Exon 1.16  PDB: B:98-132           --------------------------Exon 1.18a        Exon 1.19  PDB: B:177-204   Exon 1.20a  PDB: B:205-238        -------------------------------------------Exon 1.22b  PDB: B:282-333 UniProt: 282-333         Exon 1.23a              Exon 1.23c  PDB: B:358-386   Exon 1.24a  PDB: B:387-414   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.17  PDB: B:132-158  -------------------------------------------------------------------------------Exon 1.21b  PDB: B:238-281 UniProt: 238-281 ------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3brw B  78 KVKLECNPTARIYRKHFLGKEHFNYYSLDTALGHLVFSLKYDVIGDQEHLRLLLRTKCRTYHDVIPISCLTEFPNVVQMAKLVCEDVNVDRFYPVLYPKASRLIVTFDEHVISNNFKFGVIYQKLGATSEEELFSTNEESPAFVEFLEFLGQKVKLQDFKGFRGGLDVTHGQTGTESVYCNFRNKEIMFHVSTKLPYTEGDAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASNFLHAYVVVQAEGGGPDGPLYKVSVTARDDVPFFGPPLPDPAVFRKGPEFQEFLLTKLINAEYACYKAEKFAKLEERTRAALLETLYEELHIHSQSMMGLGGD 414
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407

Chain C from PDB  Type:PROTEIN  Length:332
 aligned with RPGP1_HUMAN | P47736 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:336
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407      
          RPGP1_HUMAN    78 KVKLECNPTARIYRKHFLGKEHFNYYSLDAALGHLVFSLKYDVIGDQEHLRLLLRTKCRTYHDVIPISCLTEFPNVVQMAKLVCEDVNVDRFYPVLYPKASRLIVTFDEHVISNNFKFGVIYQKLGQTSEEELFSTNEESPAFVEFLEFLGQKVKLQDFKGFRGGLDVTHGQTGTESVYCNFRNKEIMFHVSTKLPYTEGDAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASNFLHAYVVVQAEGGGPDGPLYKVSVTARDDVPFFGPPLPDPAVFRKGPEFQEFLLTKLINAEYACYKAEKFAKLEERTRAALLETLYEELHIHSQSMMGLGG 413
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhh....eeeeeeee...eeeeeeeeeeee..eeeeeeeeee...eeeee..........hhhhhhhhhh........ee....hhhhhhhhhhh.....eeeeeeee.............................eee......................eeeee....eeeeee.hhh..............hhhhh.eeeee..................eeeee.....----.............................hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------T-----------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------RAPGAP  PDB: C:181-397 UniProt: 181-397                                                                                                                                                                                  ---------------- PROSITE (2)
           Transcript 1 (1) Exon 1.15b          Exon 1.16  PDB: C:98-132           --------------------------Exon 1.18a        Exon 1.19  PDB: C:177-204   Exon 1.20a  PDB: C:205-238        -------------------------------------------Exon 1.22b  PDB: C:282-333 (gaps) UniProt: 282-333  Exon 1.23a              Exon 1.23c  PDB: C:358-386   Exon 1.24a  PDB: C:387-413  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.17  PDB: C:132-158  -------------------------------------------------------------------------------Exon 1.21b  PDB: C:238-281 UniProt: 238-281 ------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3brw C  78 KVKLECNPTARIYRKHFLGKEHFNYYSLDTALGHLVFSLKYDVIGDQEHLRLLLRTKCRTYHDVIPISCLTEFPNVVQMAKLVCEDVNVDRFYPVLYPKASRLIVTFDEHVISNNFKFGVIYQKLGATSEEELFSTNEESPAFVEFLEFLGQKVKLQDFKGFRGGLDVTHGQTGTESVYCNFRNKEIMFHVSTKLPYTEGDAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASNFLHAYVVVQAEGG----PLYKVSVTARDDVPFFGPPLPDPAVFRKGPEFQEFLLTKLINAEYACYKAEKFAKLEERTRAALLETLYEELHIHSQSMMGLGG 413
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       | -  |    337       347       357       367       377       387       397       407      
                                                                                                                                                                                                                                                                                 325  330

Chain D from PDB  Type:PROTEIN  Length:167
 aligned with RAP1B_HUMAN | P61224 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
          RAP1B_HUMAN     1 MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3brwD00 D:1-167 P-loop containing nucleotide triphosphate hydrolases                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh...........eeeeeeee....eeeeeeee......hhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eeee.........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAS  PDB: D:1-167 UniProt: 1-184                                                                                                                                        PROSITE
               Transcript 2 Exon 2.3           Exon 2.4a  PDB: D:20-42Exon 2.5a          Exon 2.6  PDB: D:62-108 UniProt: 62-108        Exon 2.7a  PDB: D:109-156 UniProt: 109-156      Exon 2.8    Transcript 2
                 3brw D   1 MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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 3BRW)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

3brwD00

D:1-167

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RPGP1_HUMAN | P47736)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0030695	GTPase regulator activity	Modulates the rate of GTP hydrolysis by a GTPase.
	GO:0017016	Ras GTPase binding	Interacting selectively and non-covalently with any member of the Ras superfamily of monomeric GTPases.
	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:1990792	cellular response to glial cell derived neurotrophic factor	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 glial cell derived neurotrophic factor stimulus.
	GO:1904425	negative regulation of GTP binding	Any process that stops, prevents or reduces the frequency, rate or extent of GTP binding.
	GO:1903697	negative regulation of microvillus assembly	Any process that stops, prevents or reduces the frequency, rate or extent of microvillus assembly.
	GO:0045665	negative regulation of neuron differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
	GO:1904442	negative regulation of thyroid gland epithelial cell proliferation	Any process that stops, prevents or reduces the frequency, rate or extent of thyroid gland epithelial cell proliferation.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0051056	regulation of small GTPase mediated signal transduction	Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
	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.
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:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	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:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

Chain D (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.

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	RPGP1_HUMAN \| P47736
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UniProtKB/Swiss-Prot
	RAP1B_HUMAN \| P61224	:	3cf6 4dxa 4hdo 4hdq 4m8n 4mgi 4mgk 4mgy 4mgz 4mh0 5kho
	RPGP1_HUMAN \| P47736	:	1srq

1srq	CRYSTAL STRUCTURE OF THE RAP1GAP CATALYTIC DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

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Exons (17, 39)

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