8c83

Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

OTU domain-containing protein 2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OTU2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain x； PDBConstruct 1–307； UniProt 1–307

Ubiquitin

Saccharomyces cerevisiae

UniProt P05759

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS31_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain y； PDBConstruct 1–76； UniProt 1–76

40S ribosomal protein S0-A

OrganismNot specified

UniProt P32905

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RSSA1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–252； UniProt 1–252

40S ribosomal protein S2

OrganismNot specified

UniProt P25443

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS2_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain R； PDBConstruct 1–254； UniProt 1–254

40S ribosomal protein S4-A

OrganismNot specified

UniProt P0CX35

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS4A_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain S； PDBConstruct 1–261； UniProt 1–261

40S ribosomal protein S6-A

OrganismNot specified

UniProt P0CX37

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS6A_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain T； PDBConstruct 1–236； UniProt 1–236

40S ribosomal protein S7-A

OrganismNot specified

UniProt P26786

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS7A_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain U； PDBConstruct 1–190； UniProt 1–190

40S ribosomal protein S8-B

OrganismNot specified

UniProt P0CX40

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS8B_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain V； PDBConstruct 1–200； UniProt 1–200

40S ribosomal protein S9-A

OrganismNot specified

UniProt O13516

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS9A_YEAST
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain W； PDBConstruct 1–197； UniProt 1–197

40S ribosomal protein S11-A

OrganismNot specified

UniProt P0CX47

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS11A_YEAST
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain X； PDBConstruct 1–156； UniProt 1–156

40S ribosomal protein S13

OrganismNot specified

UniProt P05756

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS13_YEAST
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain Y； PDBConstruct 1–151； UniProt 1–151

40S ribosomal protein S21-A

OrganismNot specified

UniProt P0C0V8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS21A_YEAST
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain a； PDBConstruct 1–87； UniProt 1–87

40S ribosomal protein S22-A

OrganismNot specified

UniProt P0C0W1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS22A_YEAST
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain b； PDBConstruct 1–130； UniProt 1–130

40S ribosomal protein S23-A

OrganismNot specified

UniProt P0CX29

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS23A_YEAST
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain c； PDBConstruct 1–145； UniProt 1–145

40S ribosomal protein S24-A

OrganismNot specified

UniProt P0CX31

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S27-A × 1 （P35997） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS24A_YEAST
Isoform	—
PDB entities	16
Chains and sequence ranges	Author chain d； PDBConstruct 1–135； UniProt 1–135

40S ribosomal protein S27-A

OrganismNot specified

UniProt P35997

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S30-A × 1 （P0CX33）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS27A_YEAST
Isoform	—
PDB entities	17
Chains and sequence ranges	Author chain f； PDBConstruct 1–82； UniProt 1–82

40S ribosomal protein S30-A

OrganismNot specified

UniProt P0CX33

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 1	OTU domain-containing protein 2 × 1 （P38747） Ubiquitin × 1 （P05759） 18S ribosomal RNA × 1 40S ribosomal protein S0-A × 1 （P32905） 40S ribosomal protein S2 × 1 （P25443） 40S ribosomal protein S4-A × 1 （P0CX35） 40S ribosomal protein S6-A × 1 （P0CX37） 40S ribosomal protein S7-A × 1 （P26786） 40S ribosomal protein S8-B × 1 （P0CX40） 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S11-A × 1 （P0CX47） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S21-A × 1 （P0C0V8） 40S ribosomal protein S22-A × 1 （P0C0W1） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S24-A × 1 （P0CX31） 40S ribosomal protein S27-A × 1 （P35997）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS30A_YEAST
Isoform	—
PDB entities	18
Chains and sequence ranges	Author chain g； PDBConstruct 1–63； UniProt 1–63

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8c83
Deposition date deposition_date	2023-01-18
Structure title title	Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex
Keywords keywords	40S, Ubiquitin, Deubiquitinating enzyme, Otu2, Rps7, RIBOSOME; RIBOSOME
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8c83__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8c83__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8c83__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	58.91 Å
Rg (electron density)	59.38 Å
Total Rg	59.30 Å
Atom count	45803
Residues	3902
Excluded volume	723990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8c83__assembly_1__model_1`	octadecameric （18）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (18)

Entity 1 Entity 1 polymer

Description description	OTU domain-containing protein 2
Molecular weight formula_weight	36157.0 kDa
Mutation mutation	C178S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	x
Atom count atom_count	45803

MTGMESGENLENMEDILARHRKENKDLQNKITGMKKQATKSKRKEVNSKCLDLQDKLKTKQENEIRDWKIANNEVFDAEQEDEVTPEKLLEQLSISRDEKEQQNVPVQQQQQGQTKKRRNRQKERLAKRDAAIAKMKEEAALEASKQPDLKKMEQESIDQLCELKKLKQFDIQPDGHSLFASILDQLKLRHDPKKLDQDMDVMKLRWLSCNYVQEHRDDFIPYLFDEETMKMKDIDEYTKEMEHTAQWGGEIEILALSHVFDCPISILMSGRPIQVYNECGKNPELKLVYYKHSYALGEHYNSLHDS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escharichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	y

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	18S ribosomal RNA
Molecular weight formula_weight	579871.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	2

UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCGAUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCGCCACGUCCAGACACAAUAAGGAUUGACCGAUUGAGAGCUCUUUCUUGAUUUUGUGGCUGGUAGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAGAAGGAAGGGCAACUUAACCAUCUACAGAGCGGUGCUAGAAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUAGAGGAACUAACAAGUCUGUAAUGCCCUUAGAGGUUCUGGGCCGUACGCGUGCAACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Entity 4 Entity 4 polymer

Description description	40S ribosomal protein S0-A
Molecular weight formula_weight	28051.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLVIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREVLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEATEWAEENADNVEW

Entity 5 Entity 5 polymer

Description description	40S ribosomal protein S2
Molecular weight formula_weight	27490.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASAQKKRF

Entity 6 Entity 6 polymer

Description description	40S ribosomal protein S4-A
Molecular weight formula_weight	29469.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEERDRRRAQQGL

Entity 7 Entity 7 polymer

Description description	40S ribosomal protein S6-A
Molecular weight formula_weight	27054.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQGFPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQELEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVTPQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Entity 8 Entity 8 polymer

Description description	40S ribosomal protein S7-A
Molecular weight formula_weight	21658.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVFEIPSETH

Entity 9 Entity 9 polymer

Description description	40S ribosomal protein S8-B
Molecular weight formula_weight	22537.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRIETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQTLGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDGYILEGEELAFYLRRLTAKK

Entity 10 Entity 10 polymer

Description description	40S ribosomal protein S9-A
Molecular weight formula_weight	22487.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKAEASGEAADEADEADEE

Entity 11 Entity 11 polymer

Description description	40S ribosomal protein S11-A
Molecular weight formula_weight	17785.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MSTELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFTGLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQCRPISKTVRFNVVKVSAAAGKANKQFAKF

Entity 12 Entity 12 polymer

Description description	40S ribosomal protein S13
Molecular weight formula_weight	17059.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN

Entity 13 Entity 13 polymer

Description description	40S ribosomal protein S21-A
Molecular weight formula_weight	9758.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVDEEGRAIPGEYVTYALSGYVRSRGESDDSLNRLAQNDGLLKNVWSYSR

Entity 14 Entity 14 polymer

Description description	40S ribosomal protein S22-A
Molecular weight formula_weight	14650.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

MTRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGKIVVQLNGRLNKCGVISPRFNVKIGDIEKWTANLLPARQFGYVILTTSAGIMDHEEARRKHVSGKILGFVY

Entity 15 Entity 15 polymer

Description description	40S ribosomal protein S23-A
Molecular weight formula_weight	16073.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c

MGKGKPRGLNSARKLRVHRRNNRWAENNYKKRLLGTAFKSSPFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS

Entity 16 Entity 16 polymer

Description description	40S ribosomal protein S24-A
Molecular weight formula_weight	15362.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

MSDAVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKAEKDAVSVFGFRTQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVRYGLAEKVEKASRQQRKQKKNRDKKIFGTGKRLAKKVARRNAD

Entity 17 Entity 17 polymer

Description description	40S ribosomal protein S27-A
Molecular weight formula_weight	8893.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f

MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCSTILCTPTGGKAKLSEGTSFRRK

Entity 18 Entity 18 polymer

Description description	40S ribosomal protein S30-A
Molecular weight formula_weight	7137.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	g

MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRRMNPGPSVQ

▼

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	8c83P01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	8c83x01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	8c83y01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	31646

Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

OTU domain-containing protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

40S ribosomal protein S0-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

40S ribosomal protein S2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

40S ribosomal protein S4-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

40S ribosomal protein S6-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

40S ribosomal protein S7-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

40S ribosomal protein S8-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

40S ribosomal protein S9-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

40S ribosomal protein S11-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer