3RZW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MONOBODY YSMB-9 BOUND TO HUMAN SUMO1

Authors :   R. N. Gilbreth, S. Koide

Date :   12 May 11 (Deposition) - 28 Dec 11 (Release) - 23 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Beta Sandwich, Beta Grasp, Antibody Mimic, Engineered Binding Protein, Post-Translational Modification, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Koide, J. Wojcik, R. N. Gilbreth, R. J. Hoey, S. Koide
Teaching An Old Scaffold New Tricks: Monobodies Constructed Using Alternative Surfaces Of The Fn3 Scaffold.
J. Mol. Biol. V. 415 393 2012
PubMed-ID: 22198408 | Reference-DOI: 10.1016/J.JMB.2011.12.019

Molecule 1 - MONOBODY YSMB-9
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHFT2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET24A DERIVED
	Gene	:	SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-CL.43
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - SMALL UBIQUITIN-RELATED MODIFIER 1
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHFT2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET24A DERIVED
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SUMO-1, GAP-MODIFYING PROTEIN 1, GMP1, SMT3 HOMOLOG 3, SENTRIN, UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1, UBIQUITIN-LIKE PROTEIN SMT3C, SMT3C, UBIQUITIN-LIKE PROTEIN UBL1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:17 , LEU B:18	BINDING SITE FOR RESIDUE GOL B 91
2	AC2	SOFTWARE	TYR B:36 , THR B:58 , SER B:60 , GLN D:92 , GLN D:94	BINDING SITE FOR RESIDUE GOL B 92

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

Asymmetric Unit

No.	Residues
1	Val A:4	-	Pro A:5
2	Val B:4	-	Pro B:5

(no "SAP(SNP)/Variant" information available for 3RZW)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SUMO1_HUMAN	20-97	2	C:20-94 D:20-97

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SUMO1_HUMAN	20-97	1	- D:20-97

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SUMO1_HUMAN	20-97	1	C:20-94 -

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000392246	1a	ENSE00001771214	chr2:203103331-203103163	169	SUMO1_HUMAN	1-4	4	0	-	-
1.5	ENST00000392246	5	ENSE00001634753	chr2:203084829-203084755	75	SUMO1_HUMAN	5-29	25	2	C:20-29 D:20-29	10 10
1.6b	ENST00000392246	6b	ENSE00001733147	chr2:203079157-203079080	78	SUMO1_HUMAN	30-55	26	2	C:30-55 D:30-55	26 26
1.7b	ENST00000392246	7b	ENSE00001777388	chr2:203075529-203075458	72	SUMO1_HUMAN	56-79	24	2	C:56-79 D:56-79	24 24
1.9j	ENST00000392246	9j	ENSE00001390654	chr2:203072044-203070903	1142	SUMO1_HUMAN	80-101	22	2	C:80-94 D:80-97	15 18

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:89
                                                                                                                        
               SCOP domains d3rzwa_ A: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..eeeeeee.......eeeeeeee.......eeeeee....eeee.......eeeeeeeeee..ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3rzw A  2 SSVPTKLEVVAATPTSLLISWDAGYWFIDYYRITYGETGGNSPVQEFTVPGYSSTATISGLSPGVDYTITVYAYYDNYGWSPISINYRT 90
                                    11        21        31        41        51        61        71        81

Chain B from PDB  Type:PROTEIN  Length:89
                                                                                                                        
               SCOP domains d3rzwb_ B: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..eeeeeee.......eeeeeeee.......eeeeee....eeee.......eeeeeeeeee..ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3rzw B  2 SSVPTKLEVVAATPTSLLISWDAGYWFIDYYRITYGETGGNSPVQEFTVPGYSSTATISGLSPGVDYTITVYAYYDNYGWSPISINYRT 90
                                    11        21        31        41        51        61        71        81

Chain C from PDB  Type:PROTEIN  Length:75
 aligned with SUMO1_HUMAN | P63165 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:75
                                    29        39        49        59        69        79        89     
           SUMO1_HUMAN   20 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ 94
               SCOP domains d3rzwc_ C: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeee....hhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: C:20-94 UniProt: 20-97                                    PROSITE
               Transcript 1 Exon 1.5  Exon 1.6b  PDB: C:30-55   Exon 1.7b  PDB: C:56-79 Exon 1.9j       Transcript 1
                  3rzw C 20 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYAQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ 94
                                    29        39        49        59        69        79        89

Chain D from PDB  Type:PROTEIN  Length:78
 aligned with SUMO1_HUMAN | P63165 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:78
                                    29        39        49        59        69        79        89        
           SUMO1_HUMAN   20 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG 97
               SCOP domains d3rzwd_ D: automated matches                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeee....hhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: D:20-97 UniProt: 20-97                                       PROSITE
               Transcript 1 Exon 1.5  Exon 1.6b  PDB: D:30-55   Exon 1.7b  PDB: D:56-79 Exon 1.9j          Transcript 1
                  3rzw D 20 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYAQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG 97
                                    29        39        49        59        69        79        89

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: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Fibronectin type III (212)

Family: automated matches (32)

Protein domain: automated matches (32)

Human (Homo sapiens) [TaxId: 9606] (26)

1a	d3rzwa_	A:
1b	d3rzwb_	B:

Class: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: Ubiquitin-related (337)

Protein domain: automated matches (80)

Human (Homo sapiens) [TaxId: 9606] (62)

2a	d3rzwc_	C:
2b	d3rzwd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

Chain C,D (SUMO1_HUMAN | P63165)

molecular function
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	GO:0015459	potassium channel regulator activity	Modulates potassium channel activity via direct interaction interaction with a potassium channel (binding or modification).
	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:0031386	protein tag	A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0030578	PML body organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of PML bodies, a class of nuclear body; they react against SP100 auto-antibodies (PML = promyelocytic leukemia).
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0043392	negative regulation of DNA binding	Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
	GO:0045759	negative regulation of action potential	Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
	GO:1902260	negative regulation of delayed rectifier potassium channel activity	Any process that stops, prevents or reduces the frequency, rate or extent of delayed rectifier potassium channel activity.
	GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0060021	palate development	The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
	GO:1901896	positive regulation of calcium-transporting ATPase activity	Any process that activates or increases the frequency, rate or extent of calcium-transporting ATPase activity.
	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0031334	positive regulation of protein complex assembly	Any process that activates or increases the frequency, rate or extent of protein complex assembly.
	GO:0090204	protein localization to nuclear pore	A process in which a protein is transported to, or maintained in, a nuclear pore.
	GO:0050821	protein stabilization	Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
	GO:1903169	regulation of calcium ion transmembrane transport	Any process that modulates the frequency, rate or extent of calcium ion transmembrane transport.
	GO:0086004	regulation of cardiac muscle cell contraction	Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.
	GO:0060334	regulation of interferon-gamma-mediated signaling pathway	Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.
	GO:0032880	regulation of protein localization	Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
	GO:0031647	regulation of protein stability	Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0016605	PML body	A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
	GO:0001741	XY body	A structure found in a male mammalian spermatocyte containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0001650	fibrillar center	A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0016604	nuclear body	Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
	GO:0008076	voltage-gated potassium channel complex	A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

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	3rzw
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