2GM3 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN UNIVERSAL STRESS PROTEIN FAMILY PROTEIN FROM ARABIDOPSIS THALIANA AT3G01520 WITH AMP BOUND

Authors :   E. Bitto, G. E. Wesenberg, G. N. Phillips Jr. , C. A. Bingman, Center Fo Eukaryotic Structural Genomics (Cesg)

Date :   05 Apr 06 (Deposition) - 18 Apr 06 (Release) - 08 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.46

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: C,E  (1x)
Biol. Unit 5: A (1x),D (1x)
Biol. Unit 6: B (1x),F (1x)

Keywords :   At3G01520, Putative Ethylene-Responsive Protein, Usp Domain, Nucleotide Binding Domain, Amp, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. O. J. Kim, E. Bitto, C. A. Bingman, H. J. Kim, B. W. Han, G. N. Phillips
Crystal Structure Of The Protein At3G01520, A Eukaryotic Universal Stress Protein-Like Protein From Arabidopsis Thaliana In Complex With Amp.
Proteins V. 83 1368 2015
PubMed-ID: 25921306 | Reference-DOI: 10.1002/PROT.24821

Molecule 1 - UNKNOWN PROTEIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP 16
	Expression System Strain	:	BL834 P(RARE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AT3G01520
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:			C		E
Biological Unit 5 (1x)	:	A (1x)			D (1x)
Biological Unit 6 (1x)	:		B (1x)				F (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 24)

No.	Name	Count	Type	Full Name
1	AMP	6	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 8)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 8)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (2, 4)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 6 (2, 4)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:11 , VAL A:12 , ASN A:13 , SER A:26 , CYS A:27 , LEU A:51 , VAL A:53 , PRO A:112 , VAL A:130 , GLY A:131 , ARG A:133 , VAL A:146 , SER A:147	BINDING SITE FOR RESIDUE AMP A 176
2	AC2	SOFTWARE	ALA B:11 , VAL B:12 , ASN B:13 , SER B:26 , CYS B:27 , LEU B:51 , VAL B:53 , PRO B:112 , ILE B:116 , VAL B:130 , GLY B:131 , ARG B:133 , THR B:145 , VAL B:146 , SER B:147	BINDING SITE FOR RESIDUE AMP B 176
3	AC3	SOFTWARE	ALA C:11 , VAL C:12 , ASN C:13 , SER C:26 , CYS C:27 , LEU C:51 , VAL C:53 , VAL C:130 , GLY C:131 , ARG C:133 , THR C:145 , VAL C:146 , SER C:147	BINDING SITE FOR RESIDUE AMP C 176
4	AC4	SOFTWARE	ALA D:11 , VAL D:12 , ASN D:13 , SER D:26 , CYS D:27 , LEU D:51 , VAL D:53 , ILE D:116 , VAL D:130 , GLY D:131 , SER D:132 , ARG D:133 , THR D:145 , VAL D:146 , SER D:147	BINDING SITE FOR RESIDUE AMP D 176
5	AC5	SOFTWARE	ALA E:11 , VAL E:12 , ASN E:13 , SER E:26 , CYS E:27 , LEU E:51 , HIS E:52 , VAL E:53 , VAL E:130 , GLY E:131 , ARG E:133 , VAL E:146 , SER E:147	BINDING SITE FOR RESIDUE AMP E 176
6	AC6	SOFTWARE	ALA F:11 , VAL F:12 , ASN F:13 , SER F:26 , CYS F:27 , LEU F:51 , HIS F:52 , VAL F:53 , PRO F:112 , VAL F:130 , GLY F:131 , SER F:132 , ARG F:133 , THR F:145 , VAL F:146 , SER F:147	BINDING SITE FOR RESIDUE AMP F 176

(no "SS Bond" information available for 2GM3)

Asymmetric Unit

No.	Residues
1	Tyr A:20	-	Pro A:21
2	Tyr B:20	-	Pro B:21
3	Tyr C:20	-	Pro C:21
4	Tyr D:20	-	Pro D:21
5	Tyr E:20	-	Pro E:21
6	Tyr F:20	-	Pro F:21

(no "SAP(SNP)/Variant" information available for 2GM3)

(no "PROSITE Motif" information available for 2GM3)

(no "Exon" information available for 2GM3)

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:153
 aligned with USPAL_ARATH | Q8LGG8 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:171
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 
          USPAL_ARATH     5 PTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDDVDSIYASPEDFRDMRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRNADETPSDPADD 175
               SCOP domains d2gm3a1 A:5-175 Putative ethylene-responsive protei          n AT3g01520/F4P13_7                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee............hhhhhhhhhhhhhhh.......eeeeeeeee.----------....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhhhhh..eeeeee....--------hhhhhhhhhh...eeeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm3 A   5 PTKVmVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQV----------SIYASPEDFRDmRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLG--------TVSAFCVKHAECPVmTIKRNADETPSDPADD 175
                                |   14        24        34        44        54|        - |      74  |     84        94       104       114       124       134 |       -|      154    |  164       174 
                                |                                            55         66         77-MSE                                                    136      145           159-MSE            
                                9-MSE

Chain B from PDB  Type:PROTEIN  Length:145
 aligned with USPAL_ARATH | Q8LGG8 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
          USPAL_ARATH     5 PTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDDVDSIYASPEDFRDMRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRNADETPSDPAD 174
               SCOP domains d2gm3b_ B: Putative ethylene-responsive protein AT3          g01520/F4P13       _7                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee............hhhhhhhhhhhhhhh.......eeeeeeeee.----------....hhhhhhhh-------hhhhhhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhhhhh..eeeeee....--------hhhhhhhhhh...eeeee.hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm3 B   5 PTKVmVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQV----------SIYASPEDFRDm-------GLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLG--------TVSAFCVKHAECPVmTIKRNADETPSDPAD 174
                                |   14        24        34        44        54|        - |      74  |      -|       94       104       114       124       134 |       -|      154    |  164       174
                                9-MSE                                        55         66         77-MSE  85                                                136      145           159-MSE

Chain C from PDB  Type:PROTEIN  Length:153
 aligned with USPAL_ARATH | Q8LGG8 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:171
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 
          USPAL_ARATH     5 PTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDDVDSIYASPEDFRDMRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRNADETPSDPADD 175
               SCOP domains d2gm3c_ C: Putative ethylene-responsive protein AT3          g01520/F4P13_7                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee............hhhhhhhhhhhhhhh.......eeeeeeeee.----------....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhhhhh..eeeeee....--------hhhhhhhhhh...eeeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm3 C   5 PTKVmVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQV----------SIYASPEDFRDmRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLG--------TVSAFCVKHAECPVmTIKRNADETPSDPADD 175
                                |   14        24        34        44        54|        - |      74  |     84        94       104       114       124       134 |       -|      154    |  164       174 
                                9-MSE                                        55         66         77-MSE                                                    136      145           159-MSE

Chain D from PDB  Type:PROTEIN  Length:153
 aligned with USPAL_ARATH | Q8LGG8 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:171
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 
          USPAL_ARATH     5 PTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDDVDSIYASPEDFRDMRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRNADETPSDPADD 175
               SCOP domains d2gm3d_ D: Putative ethylene-responsive protein AT3          g01520/F4P13_7                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee............hhhhhhhhhhhhhhh.......eeeeeeeee.----------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhh..eeeeee....--------hhhhhhhhhh...eeeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm3 D   5 PTKVmVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQV----------SIYASPEDFRDmRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLG--------TVSAFCVKHAECPVmTIKRNADETPSDPADD 175
                                |   14        24        34        44        54|        - |      74  |     84        94       104       114       124       134 |       -|      154    |  164       174 
                                9-MSE                                        55         66         77-MSE                                                    136      145           159-MSE

Chain E from PDB  Type:PROTEIN  Length:153
 aligned with USPAL_ARATH | Q8LGG8 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:171
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 
          USPAL_ARATH     5 PTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDDVDSIYASPEDFRDMRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRNADETPSDPADD 175
               SCOP domains d2gm3e_ E: Putative ethylene-responsive protein AT3          g01520/F4P13_7                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee............hhhhhhhhhhhhhhh.......eeeeeeeee.----------.ee.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhhhhh..eeeeee....--------hhhhhhhhhh...eeeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm3 E   5 PTKVmVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQV----------SIYASPEDFRDmRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLG--------TVSAFCVKHAECPVmTIKRNADETPSDPADD 175
                                |   14        24        34        44        54|        - |      74  |     84        94       104       114       124       134 |       -|      154    |  164       174 
                                9-MSE                                        55         66         77-MSE                                                    136      145           159-MSE

Chain F from PDB  Type:PROTEIN  Length:148
 aligned with USPAL_ARATH | Q8LGG8 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:171
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 
          USPAL_ARATH     5 PTKVMVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQVVDEDGFDDVDSIYASPEDFRDMRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLGRFQKVFVGTVSAFCVKHAECPVMTIKRNADETPSDPADD 175
               SCOP domains d2gm3f_ F: Putative ethylene-responsive protein AT3          g01520/F4P13_7                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee............hhhhhhhhhhhhhhh.......eeeeeeeee.----------....hhhhhhhhhh-----hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhh..eeeeee....--------hhhhhhhhhh...eeeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm3 F   5 PTKVmVAVNASTIKDYPNPSISCKRAFEWTLEKIVRSNTSDFKILLLHVQV----------SIYASPEDFRDmRQ-----GLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKRVRPDFLVVGSRGLG--------TVSAFCVKHAECPVmTIKRNADETPSDPADD 175
                                |   14        24        34        44        54|        - |      74  | |    -|       94       104       114       124       134 |       -|      154    |  164       174 
                                9-MSE                                        55         66         77-MSE  85                                                136      145           159-MSE            
                                                                                                     79

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Adenine nucleotide alpha hydrolases-like (110)

Family: Universal stress protein-like (10)

Protein domain: Putative ethylene-responsive protein AT3g01520/F4P13_7 (1)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (1)

1a	d2gm3a1	A:5-175
1b	d2gm3b_	B:
1c	d2gm3c_	C:
1d	d2gm3d_	D:
1e	d2gm3e_	E:
1f	d2gm3f_	F:

(no "CATH Domain" information available for 2GM3)

(no "Pfam Domain" information available for 2GM3)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (USPAL_ARATH | Q8LGG8)

molecular function
	GO:0016208	AMP binding	Interacting selectively and non-covalently with AMP, adenosine monophosphate.
biological process
	GO:0006950	response to stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
	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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		Tyr F:20 - Pro F:21	[ RasMol ]

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	2gm3
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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 24)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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