3EVX - 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 :   CRYSTAL STRUCTURE OF THE HUMAN E2-LIKE UBIQUITIN-FOLD MODIFIER CONJUGATING ENZYME 1 (UFC1). NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR41

Authors :   F. Forouhar, M. Abashidze, J. Seetharaman, C. K. Ho, H. Janjua, K. Cunningham, L-. C. Ma, R. Xiao, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelinoe, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   13 Oct 08 (Deposition) - 21 Oct 08 (Release) - 07 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.54

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 :   Alpha-Beta Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Polymorphism, Ubl Conjugation Pathway, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Liu, F. Forouhar, A. Eletsky, H. S. Atreya, J. M. Aramini, R. Xiao, Y. J. Huang, M. Abashidze, J. Seetharaman, J. Liu, B. Rost, T. Acton, G. T. Montelione, J. F. Hunt, T. Szyperski
Nmr And X-Ray Structures Of Human E2-Like Ubiquitin-Fold Modifier Conjugating Enzyme 1 (Ufc1) Reveal Structural And Functional Conservation In The Metazoan Ufm1-Uba5-Ufc1 Ubiquination Pathway.
J. Struct. Funct. Genom. V. 10 127 2009
PubMed-ID: 19101823 | Reference-DOI: 10.1007/S10969-008-9054-7
(for further references see the PDB file header)

Molecule 1 - UFM1-CONJUGATING ENZYME 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CGI-126, HSPC155, UFC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UBIQUITIN-FOLD MODIFIER-CONJUGATING ENZYME 1

		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 (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	SCN	4	Ligand/Ion	THIOCYANATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 4 (2, 3)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SCN	1	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:76 , LYS A:77 , HIS A:161 , ARG C:25 , GLU C:26 , VAL C:29	BINDING SITE FOR RESIDUE SCN A 176
2	AC2	SOFTWARE	LEU B:76 , LYS B:77 , HIS B:161 , ARG D:25 , VAL D:29	BINDING SITE FOR RESIDUE SCN B 176
3	AC3	SOFTWARE	ARG A:25 , VAL A:29 , LEU C:76 , LYS C:77 , HIS C:161	BINDING SITE FOR RESIDUE SCN C 176
4	AC4	SOFTWARE	ARG B:25 , VAL B:29 , LEU D:76 , LYS D:77 , HIS D:161	BINDING SITE FOR RESIDUE SCN D 176

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

Asymmetric Unit

No.	Residues
1	Tyr A:90	-	Pro A:91
2	Val A:129	-	Pro A:130
3	Tyr B:90	-	Pro B:91
4	Val B:129	-	Pro B:130
5	Tyr C:90	-	Pro C:91
6	Val C:129	-	Pro C:130
7	Tyr D:90	-	Pro D:91
8	Val D:129	-	Pro D:130

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028312	Y	90	C	UFC1_HUMAN	Polymorphism	17849932	A/B/C/D	Y	90	C

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028312	Y	90	C	UFC1_HUMAN	Polymorphism	17849932	A	Y	90	C

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028312	Y	90	C	UFC1_HUMAN	Polymorphism	17849932	B	Y	90	C

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

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028312	Y	90	C	UFC1_HUMAN	Polymorphism	17849932	C	Y	90	C

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

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028312	Y	90	C	UFC1_HUMAN	Polymorphism	17849932	D	Y	90	C

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

(no "PROSITE Motif" information available for 3EVX)

Asymmetric Unit (6, 24)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000368003	3a	ENSE00001446105	chr1:161123542-161123910	369	UFC1_HUMAN	1-41	41	4	A:5-41 B:5-41 C:5-41 D:5-41	37 37 37 37
1.4a	ENST00000368003	4a	ENSE00000958732	chr1:161126740-161126807	68	UFC1_HUMAN	42-64	23	4	A:42-64 B:42-64 C:42-64 D:42-64	23 23 23 23
1.4c	ENST00000368003	4c	ENSE00001132692	chr1:161127044-161127107	64	UFC1_HUMAN	64-85	22	4	A:64-85 B:64-85 C:64-85 D:64-85	22 22 22 22
1.5a	ENST00000368003	5a	ENSE00001132687	chr1:161127407-161127483	77	UFC1_HUMAN	86-111	26	4	A:86-111 B:86-111 C:86-111 D:86-111	26 26 26 26
1.5d	ENST00000368003	5d	ENSE00001132682	chr1:161127911-161128001	91	UFC1_HUMAN	111-141	31	4	A:111-141 B:111-141 C:111-141 D:111-141	31 31 31 31
1.6b	ENST00000368003	6b	ENSE00001446104	chr1:161128202-161128646	445	UFC1_HUMAN	142-167	26	4	A:142-162 B:142-162 C:142-162 D:142-162	21 21 21 21

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:158
 aligned with UFC1_HUMAN | Q9Y3C8 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:158
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154        
           UFC1_HUMAN     5 ATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHK 162
               SCOP domains d3evxa_ A: Ufm1-conjugating enzyme 1, UFC1                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeeee..eeeeeeeeee.............hhhhh......hhhhh.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------C------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:5-41 UniProt: 1-41 Exon 1.4a  PDB: A:42-64---------------------Exon 1.5a  PDB: A:86-111  ------------------------------Exon 1.6b             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.4c  PDB: A:64-8-------------------------Exon 1.5d  PDB: A:111-141      --------------------- Transcript 1 (2)
                 3evx A   5 ATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKmYRGGKICLTDHFKPLWARNVPKFGLAHLmALGLGPWLAVEIPDLIQKGVIQHK 162
                                    14        24        34        44        54        64        74        84        94       104    |  114       124       134   |   144       154        
                                                                                                                                  109-MSE                      138-MSE

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with UFC1_HUMAN | Q9Y3C8 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:158
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154        
           UFC1_HUMAN     5 ATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHK 162
               SCOP domains d3evxb_ B: Ufm1-conjugating enzyme 1, UFC1                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeeee..eeeeeeeeee.............hhhhh......hhhhh.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------C------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: B:5-41 UniProt: 1-41 Exon 1.4a  PDB: B:42-64---------------------Exon 1.5a  PDB: B:86-111  ------------------------------Exon 1.6b             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.4c  PDB: B:64-8-------------------------Exon 1.5d  PDB: B:111-141      --------------------- Transcript 1 (2)
                 3evx B   5 ATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKmYRGGKICLTDHFKPLWARNVPKFGLAHLmALGLGPWLAVEIPDLIQKGVIQHK 162
                                    14        24        34        44        54        64        74        84        94       104    |  114       124       134   |   144       154        
                                                                                                                                  109-MSE                      138-MSE

Chain C from PDB  Type:PROTEIN  Length:158
 aligned with UFC1_HUMAN | Q9Y3C8 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:158
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154        
           UFC1_HUMAN     5 ATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHK 162
               SCOP domains d3evxc_ C: Ufm1-conjugating enzyme 1, UFC1                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeeee..eeeeeeeeee.............hhhhh......hhhhh.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------C------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: C:5-41 UniProt: 1-41 Exon 1.4a  PDB: C:42-64---------------------Exon 1.5a  PDB: C:86-111  ------------------------------Exon 1.6b             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.4c  PDB: C:64-8-------------------------Exon 1.5d  PDB: C:111-141      --------------------- Transcript 1 (2)
                 3evx C   5 ATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKmYRGGKICLTDHFKPLWARNVPKFGLAHLmALGLGPWLAVEIPDLIQKGVIQHK 162
                                    14        24        34        44        54        64        74        84        94       104    |  114       124       134   |   144       154        
                                                                                                                                  109-MSE                      138-MSE

Chain D from PDB  Type:PROTEIN  Length:158
 aligned with UFC1_HUMAN | Q9Y3C8 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:158
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154        
           UFC1_HUMAN     5 ATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHK 162
               SCOP domains d3evxd_ D: Ufm1-conjugating enzyme 1, UFC1                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeeee..eeeeeeeeee.............hhhhh......hhhhh.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------C------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: D:5-41 UniProt: 1-41 Exon 1.4a  PDB: D:42-64---------------------Exon 1.5a  PDB: D:86-111  ------------------------------Exon 1.6b             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.4c  PDB: D:64-8-------------------------Exon 1.5d  PDB: D:111-141      --------------------- Transcript 1 (2)
                 3evx D   5 ATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKmYRGGKICLTDHFKPLWARNVPKFGLAHLmALGLGPWLAVEIPDLIQKGVIQHK 162
                                    14        24        34        44        54        64        74        84        94       104    |  114       124       134   |   144       154        
                                                                                                                                  109-MSE                      138-MSE

Legend:		→ Mismatch	(orange background)
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	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) (23004)

Fold: UBC-like (176)

Superfamily: UBC-like (176)

Family: UFC1-like (5)

Protein domain: Ufm1-conjugating enzyme 1, UFC1 (4)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d3evxa_	A:
1b	d3evxb_	B:
1c	d3evxc_	C:
1d	d3evxd_	D:

(no "CATH Domain" information available for 3EVX)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (UFC1_HUMAN | Q9Y3C8)

molecular function
	GO:0071568	UFM1 transferase activity	Catalysis of the transfer of UFM1 from one protein to another via the reaction X-UFM1 + Y --> Y-UFM1 + X, where both X-UFM1 and Y-UFM1 are covalent linkages.
	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).
biological process
	GO:1990592	protein K69-linked ufmylation	A protein ufmylation process in which a polymer of the ubiquitin-like protein UFM1 is formed by linkages between lysine residues at position 69 of the UFM1 monomers, is added to a protein.
	GO:0071569	protein ufmylation	Covalent attachment of the ubiquitin-like protein UFM1 to another protein.
	GO:0034976	response to endoplasmic reticulum stress	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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
	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.

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	UFC1_HUMAN \| Q9Y3C8	:	2k07 2z6o 2z6p

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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