5HPY - JenaLib

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Title :   CRYSTAL STRUCTURE OF RHOA.GDP.MGF3-IN COMPLEX WITH HUMAN MYOSIN 9B RHOGAP DOMAIN

Authors :   F. S. Yi, J. Q. Ren, W. Feng

Date :   21 Jan 16 (Deposition) - 13 Jul 16 (Release) - 17 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Complex, Rho Gtpases, Rhogap, Gene Regulation-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Yi, R. Kong, J. Ren, L. Zhu, J. Lou, J. Y. Wu, W. Feng
Noncanonical Myo9B-Rhogap Accelerates Rhoa Gtp Hydrolysis B A Dual-Arginine-Finger Mechanism
J. Mol. Biol. V. 428 3043 2016
PubMed-ID: 27363609 | Reference-DOI: 10.1016/J.JMB.2016.06.014

Molecule 1 - UNCONVENTIONAL MYOSIN-IXB
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MYO9B, MYR5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UNCONVENTIONAL MYOSIN-9B

Molecule 2 - TRANSFORMING PROTEIN RHOA
	Chains	:	B, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 3-181
	Gene	:	RHOA, ARH12, ARHA, RHO12
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RHO CDNA CLONE 12,H12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:235 , GLY B:14 , ALA B:15 , LYS B:18 , PRO B:36 , THR B:37 , GLY B:62 , GLN B:63 , MG B:202 , GDP B:203 , HOH B:318 , HOH B:319	binding site for residue MGF B 201
2	AC2	SOFTWARE	THR B:19 , THR B:37 , MGF B:201 , GDP B:203 , HOH B:305 , HOH B:319	binding site for residue MG B 202
3	AC3	SOFTWARE	ARG A:235 , ARG A:340 , ALA B:15 , CYS B:16 , GLY B:17 , LYS B:18 , THR B:19 , CYS B:20 , PHE B:30 , TYR B:34 , LYS B:118 , ASP B:120 , LEU B:121 , SER B:160 , ALA B:161 , LYS B:162 , MGF B:201 , MG B:202 , HOH B:305 , HOH B:307 , HOH B:319 , HOH B:320 , HOH B:322	binding site for residue GDP B 203
4	AC4	SOFTWARE	ARG D:235 , GLY F:14 , ALA F:15 , LYS F:18 , PRO F:36 , THR F:37 , GLY F:62 , GLN F:63 , GDP F:202 , MG F:203 , HOH F:307 , HOH F:314 , HOH F:315	binding site for residue MGF F 201
5	AC5	SOFTWARE	ARG D:235 , ARG D:340 , ALA F:15 , CYS F:16 , GLY F:17 , LYS F:18 , THR F:19 , CYS F:20 , TYR F:34 , LYS F:118 , ASP F:120 , LEU F:121 , SER F:160 , ALA F:161 , LYS F:162 , MGF F:201 , MG F:203 , HOH F:307 , HOH F:315 , HOH F:325 , HOH F:336	binding site for residue GDP F 202
6	AC6	SOFTWARE	THR F:19 , THR F:37 , MGF F:201 , GDP F:202 , HOH F:307 , HOH F:315	binding site for residue MG F 203
7	AC7	SOFTWARE	THR F:19 , THR F:37 , GLU F:40 , TYR F:42 , ASP F:59 , HOH F:312	binding site for residue MG F 204

(no "SS Bond" information available for 5HPY)

Asymmetric Unit

No.	Residues
1	Gly A:196	-	His A:197
2	Asp A:362	-	Pro A:363

(no "SAP(SNP)/Variant" information available for 5HPY)

(no "PROSITE Motif" information available for 5HPY)

(no "Exon" information available for 5HPY)

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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hpy A 196 GHFGVCVSVPIVLEKLLEHVEMHGLYTEGLYRKSGAANRTRELRQALQTDPAAVKLENFPIHAITGVLKQWLRELPEPLMTFAQYGDFLRAVELPEKQEQLAAIYAVLEHLPEANHNSLERLIFHLVKVALLEDVNRMSPGALAIIFAPCLLRCSDPLTSMKDVLKITTCVEMLIKEQMRKYKVKMEEISQL 398
                                  |213       223       233       243       253       263       273       283       293       303       313       323       333       343       353   ||  366       376       386       396  
                                202|                                                                                                                                               357|                                     
                                 211                                                                                                                                                361

Chain B from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee..hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hpy B   3 AIRKKLVIVGDGACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQ 180
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain D from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hpy D 198 FGVCSVPIVLEKLLEHVEMHGLYTEGLYRKSGAANRTRELRQALQTDPAAVKLENFPIHAITGVLKQWLRELPEPLMTFAQYGDFLRAVELPEKQEQLAAIYAVLEHLPEANHNSLERLIFHLVKVALLEDVNRMSPGALAIIFAPCLLRCPSDPLTSMKDVLKITTCVEMLIKEQMRKYKVKMEEISQL 398
                               ||  216       226       236       246       256       266       276       286       296       306       316       326       336       346       356 ||    368       378       388       398
                             201|                                                                                                                                                358|                                     
                              211                                                                                                                                                 361

Chain F from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhh......hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hpy F   3 AIRKKLVIVGDGACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQ 180
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

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 5HPY)

(no "CATH Domain" information available for 5HPY)

(no "Pfam Domain" information available for 5HPY)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:362 - Pro A:363	[ RasMol ]
		Gly A:196 - His A:197	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	5hpy
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(no "Related Entries Specified in the PDB File" available for 5HPY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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