7nad

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model

Method: ELECTRON MICROSCOPY

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

RRP17 isoform 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q2X9_YEASX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 5； PDBConstruct 1–235； UniProt 1–235

NOC2 isoform 1

OrganismNot specified

UniProt A0A8H4BX61

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4BX61_YEASX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain 8； PDBConstruct 1–710； UniProt 1–710

60S ribosomal protein L3

OrganismNot specified

UniProt P14126

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL3_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–387； UniProt 1–387

RPL8A isoform 1

OrganismNot specified

UniProt A0A8H4C0K3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4C0K3_YEASX
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–256； UniProt 1–256

NOC3 isoform 1

OrganismNot specified

UniProt A0A8H4BYD1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4BYD1_YEASX
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain I； PDBConstruct 1–663； UniProt 1–663

60S ribosomal protein L17-A

OrganismNot specified

UniProt P05740

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL17A_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain P； PDBConstruct 1–184； UniProt 1–184

60S ribosomal protein L19-A

OrganismNot specified

UniProt P0CX82

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL19A_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain R； PDBConstruct 1–189； UniProt 1–189

60S ribosomal protein L22-A

OrganismNot specified

UniProt P05749

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL22A_YEAST
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain U； PDBConstruct 1–121； UniProt 1–121

60S ribosomal protein L25

OrganismNot specified

UniProt P04456

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL25_YEAST
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain X； PDBConstruct 1–142； UniProt 1–142

60S ribosomal protein L27-A

OrganismNot specified

UniProt P0C2H6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL27A_YEAST
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain Z； PDBConstruct 1–136； UniProt 1–136

Nucleolar GTP-binding protein 1

OrganismNot specified

UniProt Q02892

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOG1_YEAST
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain b； PDBConstruct 1–647； UniProt 1–647

60S ribosomal protein L30

OrganismNot specified

UniProt P14120

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL30_YEAST
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain c； PDBConstruct 1–105； UniProt 1–105

60S ribosomal protein L31-A

OrganismNot specified

UniProt P0C2H8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL31A_YEAST
Isoform	—
PDB entities	16
Chains and sequence ranges	Author chain d； PDBConstruct 1–113； UniProt 1–113

60S ribosomal protein L34-A

OrganismNot specified

UniProt P87262

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL34A_YEAST
Isoform	—
PDB entities	17
Chains and sequence ranges	Author chain g； PDBConstruct 1–121； UniProt 1–121

RPL38 isoform 1

OrganismNot specified

UniProt A0A6A5PUL8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5PUL8_YEASX
Isoform	—
PDB entities	18
Chains and sequence ranges	Author chain k； PDBConstruct 1–78； UniProt 1–78

YTM1 isoform 1

OrganismNot specified

UniProt A0A8H4BV53

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4BV53_YEASX
Isoform	—
PDB entities	21
Chains and sequence ranges	Author chain p； PDBConstruct 1–460； UniProt 1–460

RLP7 isoform 1

OrganismNot specified

UniProt A0A8H4BY26

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4BY26_YEASX
Isoform	—
PDB entities	22
Chains and sequence ranges	Author chain t； PDBConstruct 1–322； UniProt 1–322

Ribosome biogenesis protein RLP24

OrganismNot specified

UniProt A0A6A5PUP3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5PUP3_YEASX
Isoform	—
PDB entities	23
Chains and sequence ranges	Author chain u； PDBConstruct 1–199； UniProt 1–199

SPB1 isoform 1

OrganismNot specified

UniProt A0A8H4BSI2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） 60S ribosomal protein L37-A × 1 （P49166） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4BSI2_YEASX
Isoform	—
PDB entities	24
Chains and sequence ranges	Author chain w； PDBConstruct 1–841； UniProt 1–841

60S ribosomal protein L37-A

OrganismNot specified

UniProt P49166

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） SPB4 isoform 1 × 1 （A0A8H8UL81） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL37A_YEAST
Isoform	—
PDB entities	25
Chains and sequence ranges	Author chain j； PDBConstruct 1–88； UniProt 1–88

SPB4 isoform 1

OrganismNot specified

UniProt A0A8H8UL81

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 24 RNA 2	25S rRNA × 1 5.8S rRNA × 1 RRP17 isoform 1 × 1 （A0A6A5Q2X9） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L3 × 1 （P14126） RPL8A isoform 1 × 1 （A0A8H4C0K3） NOC3 isoform 1 × 1 （A0A8H4BYD1） 60S ribosomal protein L17-A × 1 （P05740） 60S ribosomal protein L19-A × 1 （P0CX82） 60S ribosomal protein L22-A × 1 （P05749） 60S ribosomal protein L23-A × 1 60S ribosomal protein L25 × 1 （P04456） 60S ribosomal protein L27-A × 1 （P0C2H6） Nucleolar GTP-binding protein 1 × 1 （Q02892） 60S ribosomal protein L30 × 1 （P14120） 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L34-A × 1 （P87262） RPL38 isoform 1 × 1 （A0A6A5PUL8） Ribosome biogenesis protein ERB1 × 1 Pescadillo homolog × 1 YTM1 isoform 1 × 1 （A0A8H4BV53） RLP7 isoform 1 × 1 （A0A8H4BY26） Ribosome biogenesis protein RLP24 × 1 （A0A6A5PUP3） SPB1 isoform 1 × 1 （A0A8H4BSI2） 60S ribosomal protein L37-A × 1 （P49166） ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H8UL81_YEASX
Isoform	—
PDB entities	26
Chains and sequence ranges	Author chain x； PDBConstruct 1–606； UniProt 1–606

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	7nad
Deposition date deposition_date	2021-06-21
Structure title title	State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model
Keywords keywords	ribosome biogenesis, DEAD-box ATPases, methyltransferase, nucleolus, 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.

7nad__assembly_1__model_1

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

Download this curve (.dat)

7nad__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7nad__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	58.88 Å
Rg (electron density)	60.06 Å
Total Rg	59.99 Å
Atom count	43123
Residues	4094
Excluded volume	712100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7nad__assembly_1__model_1`	26-meric （26）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (27)

Entity 1 Entity 1 polymer

Description description	25S rRNA
Molecular weight formula_weight	225356.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	1
Atom count atom_count	43123

AUGCCUGAAUAGGGUGAAGCCAGAGGAAACUCUGGUGGAGGCUCGCGAAUUUGGGUAUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACGUCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGUUUCAAAGGCCUGACAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAUAUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAGUUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUUAUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAAUCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGUCUCCAAGGUGAACAGCCUCUAGUUGAUAGAAGAUAAGGGAAGUCGGUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCACGGCCUUGGCUUGCUACAAUUAACGAUCAACUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUUAACGAGAUUCCCACUGUCCCUAUCUACUAUCUAGCGAGGCUGUCUGAUCAGGCAUUGCGUAAGCAGUAGAGUAGCCGUUACGAUCUGCUGAGA

Entity 2 Entity 2 polymer

Description description	5.8S rRNA
Molecular weight formula_weight	23067.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	2

GAACGCGCGAUACUCUUUGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUCUUUGAAAGCGUAUUGC

Entity 3 Entity 3 polymer

Description description	RRP17 isoform 1
Molecular weight formula_weight	28032.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	5

MAVHTNRQILTRGKNYATKQSKKFGTDEVTFDKDSRLDYLTGFHKRKLQRQKKAQEFIKEQERLRKIEERQKIRQERKEVMEEQLKTFKESLNLEAEIEDAKNDKTEDLQVESDESWHGFDSDKDDGDNDNNESSVKPILKKGAITEIYDDSTTVELETLEPNDNFEYLAQLNNVKLEKAEKVLKQSINRATKYAKFLGVDEKQKKKPRVKKFRYLTKNERRINQRKANDNKRRR

Entity 4 Entity 4 polymer

Description description	NOC2 isoform 1
Molecular weight formula_weight	81719.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	8

MGKVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKTDQEKADAAGTREQQQLKKSAKEEVFKDMSVETFFEKGIEIPKENKKLKKKTTKEQSDEDSSSSEEEEDMGQSMAKLAEKDPEFYKYLEENDKDLLDFAGTNPLDGIDSQDEGEDAERNSNIEEKSEQMELEKEKIELSLKLVRKWKKQLHDSPSLKLLRNIISAFKVAVNLNKEENIEDYKYAITDEKAFHELMFMVLKDVPQAIQKMAPYKIVKGARTLPNGGNVSRVSSIVKSHAGSLLILLNDITNTETAALVLHSVNELMPYLLSYRRILKELIKSIVGVWSTTRELETQIASFAFLINTTKEFKKSMLETTLKTTYSTFIKSCRKTNMRSMPLINFQKNSAAELFGIDEVLGYQVGFEYIRQLAIHLRNTMNATTKKSSKINSAEAYKIVYNWQFCHSLDFWSRVLSFACQPEKENGSESPLRQLIYPLVQVTLGVIRLIPTPQFFPLRFYLIKSLIRLSQNSGVFIPIYPLLSEILTSTAFTKAPKKSPNLAAFDFEHNIKCTQAYLNTKIYQEGLSEQFVDLLGDYFALYCKNIAFPELVTPVIISLRRYIKTSTNVKLNKRLSTVVEKLNQNSTFIQEKRSDVEFGPTNKSEVSRFLNDVAWNKTPLGSYVAVQREVKEEKARLMRESMEEQDKERETEEAKLLNSLESDDDNEDVEMSDA

Entity 5 Entity 5 polymer

Description description	60S ribosomal protein L3
Molecular weight formula_weight	43850.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL

Entity 6 Entity 6 polymer

Description description	RPL8A isoform 1
Molecular weight formula_weight	28175.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA

Entity 7 Entity 7 polymer

Description description	NOC3 isoform 1
Molecular weight formula_weight	75689.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MAKRNRSQFRIQERTAKKRKHEDSLLEGNVFQNAPEDMDENTIYSAKGSSWDEEEQDYEMVPRKNRSDTSNLVEGLPIKVNGKVERKLHKAQEKPKDDDEEDEDSNDSSEDDEGPNEEQEAEAKEDEPDTEEKILQLKEDIADLVTKVMEEPEENTAALGRLCKMVESKNPNTCKFSMLALVPVFKSIIPGYRIRPLTETEKKEKVSKEVSKLRNFEQALVYNYKNYVGRLQSLSKTPSNAAPIQVSLGILATQAAKELISTASHFNFRTDIFTLLLRRICKPRISTDPTSIQIIQTFETLLNEDEEGSISFEILRIFNKILKTRNFNIEESVLNMLLSLDVLHDYDPNTKLKGNVSAPKLKKKDRVHLSKKQRKARKEMQQIEEEMRNAEQAVSAEERERNQSEILKIVFTIYLNILKNNAKTLIGSVLEGLTKFGNMANFDLLGDFLEVMKELISDTEFDNLSSAEVRKALLCIVSAFSLISNTQYMKVNVDLSKFVDGLYALLPYICLDADIELSYRSLRLADPLNNEIIKPSVNVSTKAELLLKALDHVFFRSKSGTKERATAFTKRLYMCISHTPEKTSIAILKFIDKLMNRYPEISGLYSSEDRIGNGHFIMEADNPSRSNPEAATLWDNALLEKHYCPVVTKGLRSLSSRSKECSK

Entity 8 Entity 8 polymer

Description description	60S ribosomal protein L17-A
Molecular weight formula_weight	20589.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA

Entity 9 Entity 9 polymer

Description description	60S ribosomal protein L19-A
Molecular weight formula_weight	21762.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSKSRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLYHVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEKRDALLKEDA

Entity 10 Entity 10 polymer

Description description	60S ribosomal protein L22-A
Molecular weight formula_weight	13711.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MAPNTSRKQKIAKTFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDGTVVTVVSTAKFSGKYLKYLTKKYLKKNQLRDWIRFVSTKTNEYRLAFYQVTPEEDEEEDEE

Entity 11 Entity 11 polymer

Description description	60S ribosomal protein L23-A
Molecular weight formula_weight	4023.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

LPVGAIMNCARNLYIIMATVKKGKPELRKKVMEDNA

Entity 12 Entity 12 polymer

Description description	60S ribosomal protein L25
Molecular weight formula_weight	15787.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKKAYVRLTADYDALDIANRIGYI

Entity 13 Entity 13 polymer

Description description	60S ribosomal protein L27-A
Molecular weight formula_weight	15568.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAKKVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEERHQAGKNQWFFSKLRF

Entity 14 Entity 14 polymer

Description description	Nucleolar GTP-binding protein 1
Molecular weight formula_weight	74531.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

MQLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKVKYTGEGFVEKFEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISRAKSLVEQVARDYVRLLKFGQSLFQCKQLKRAALGRMATIVKKLRDPLAYLEQVRQHIGRLPSIDPNTRTLLICGYPNVGKSSFLRCITKSDVDVQPYAFTTKSLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSIYAIAHLRSCVLYFMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINKTDIIRPEDLDEERAQLLESVKEVPGVEIMTSSCQLEENVMEVRNKACEKLLASRIENKLKSQSRINNVLNKIHVAQPQARDDVKRTPFIPESVKNLKKYDPEDPNRRKLARDIEAENGGAGVFNVNLKDKYLLEDDEWKNDIMPEILDGKNVYDFLDPEIAAKLQALEEEEEKLENEGFYNSDDEEEIYDGFEASEVDDIKEKAAWIRNRQKTMIAEARNRKSLKNKAIMPRSKLTKSFGKMEEHMSTLGHDMSALQDKQNRAARKNRYVERGSDVVFGDQDALTASTENGVKLRQTDRLLDGVADGSMRSKADRMAKMERRERNRHAKQGESDRHNAVSLSKHLFSGKRGVGKTDFR

Entity 15 Entity 15 polymer

Description description	60S ribosomal protein L30
Molecular weight formula_weight	11430.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c

MAPVKSQESINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEYYAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA

Entity 16 Entity 16 polymer

Description description	60S ribosomal protein L31-A
Molecular weight formula_weight	12980.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

MAGLKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKGLQTVVVEEDA

Entity 17 Entity 17 polymer

Description description	60S ribosomal protein L34-A
Molecular weight formula_weight	13673.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	g

MAQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIVKKVVKEQTEAAKKSEKKAKK

Entity 18 Entity 18 polymer

Description description	RPL38 isoform 1
Molecular weight formula_weight	8845.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	k

MAREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSLYTLVINDAGKAKKLIQSLPPTLKVNRL

Entity 19 Entity 19 polymer

Description description	Ribosome biogenesis protein ERB1
Molecular weight formula_weight	48685.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	m

DHVMHLRAPKLPLDLYLAPRVRKNKLNIDPNSLIPELPSPKDLRPFPIRCSTIYAGHKGKVRTLSIDPSGLWLATGSDDGTVRVWEILTGREVYRTTLIDPKDNPDYHIECIEWNPDANNGILAVAVGENIHLIVPPIFGYDIENNGKTKIEDGFGYDTFGTVKKSNLEVNAIEWNPDANNGILAKNAVKKQVAQWNKPSQKQLEKDICITISCKKTVKKLSWHRKGDYFVTVQPDSGNTSVLIHQVSKHLTQSPFKKSKGIIMDAKFHPFKPQLFVCSQRYVRIYDLSQQILVKKLLPGARWLSKIDIHPRGDNLIASSFDKRVLWHDLDLASTPYKTLRYHEKAVRSVNFHKKLPLFSSAADDGTIHVFHATVYDDMMKNPMIVPLKKLTGHKVINSLGVLDAIWHPREAWLFSAGADNTARLWTTI

Entity 20 Entity 20 polymer

Description description	Pescadillo homolog
Molecular weight formula_weight	12445.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	n

MRIKKKNTRGNARNFITRSQAVRKLQVSLADFRRLCIFKGIYPREPRNKKKANKGSTAPTTFYYAKDIQYEEKKLKMIMMSNKQKKLYKKMKYSNAKKEEQAEN

Entity 21 Entity 21 polymer

Description description	YTM1 isoform 1
Molecular weight formula_weight	51426.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p

MTEDKSQVKIRFFTREKDELLHVQDTPMYAPISLKRYGLSEIVNHLLGSEKPVPFDFLIEGELLRTSLHDYLTKKGLSSEASLNVEYTRAILPPSYLNSFSNEDWVSSLDVGDGSKHIISGSYDGIVRTWDLSGNVQKQYSGHSGPIRAVKYISNTRLVSAGNDRTLRLWKTKNDDLKLTSQQQAQEDDDDEVNIEDGKTLAILEGHKAPVVSIDVSDNSRILSASYDNSIGFWSTIYKEMTVVDPLEDINNPNNKISTAARKRRKLTMKDGTIRRRAPLSLLESHTAPVEQVIFDSTDNTVGYSVSQDHTIKTWDLVTARCIDTRTTSYSLLSIAQLSTLNLLACGSSARHITLHDPRVGASSKVTQQQLIGHKNFVSSLDTCPENEYILCSGSHDGTVKVWDVRSTSPMYTITREDKSVQKGVNDKVFAVKWAEKVGIISAGQDKKIQINKGDNIFKN

Entity 22 Entity 22 polymer

Description description	RLP7 isoform 1
Molecular weight formula_weight	36621.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	t

MSSTQDSKAQTLNSNPEILLRKRRNADRTRIERQELAKKKREEQIKKKRSNKNKFVRAESIVAKTLATSREKERIKRVSILEDKKAKNETQHIASGKDFILKITEKANGAEENSVDLEETEEEEDDGLIREKTTYDGKPALLFIVRVRGPLAVNIPNKAFKILSLLRLVETNTGVFVKLTKNVYPLLKVIAPYVVIGKPSLSSIRSLIQKRGRIIYKGENEAEPHEIVLNDNNIVEEQLGDHGIICVEDIIHEIATMGESFSVCNFFLQPFKLNREVSGFGSLNRLRKIKQREAESRTRQFSNAATAPVIEVDIDSLLAKLN

Entity 23 Entity 23 polymer

Description description	Ribosome biogenesis protein RLP24
Molecular weight formula_weight	24027.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	u

MRIYQCHFCSSPCYPGHGIMFVRNDAKEFRFCRSKCHKAFKQRRNPRKLKWTKAFRKAAGKELAVDSTLTFAQRRNVPVRYNRELVATTLKAMARIEEIRQKRERAFYKNRMRGNKEKDFLRDKKLVESNPELLRIREVEIARKLAKEQERAESVSEQEESEEEEEDMEIDSDEEEEEQLEKQKILLKNRRRNTKKIAF

Entity 24 Entity 24 polymer

Description description	SPB1 isoform 1
Molecular weight formula_weight	96656.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	w

MGKTQKKNSKGRLDRYYYLAKEKGYRARSSFKIIQINEKYGHFLEKSKVVIDLCAAPGSWCQVASKLCPVNSLIIGVDIVPMKPMPNVITFQSDITTEDCRSKLRGYMKTWKADTVLHDGAPNVGLGWVQDAFTQSQLTLQALKLAVENLVVNGTFVTKIFRSKDYNKLIWVFQQLFEKVEATKPPASRNVSAEIFVVCKGFKAPKRLDPRLLDPKEVFEELPDGQQNMESKIYNPEKKVRKRQGYEEGDNLLYHETSILDFVRTEDPISMLGEMNKFTIDENDHEWKILKKLKQTTDEFRSCIEDLKVLGKKDFKMILRWRKIAREILGIEVKDDAKTEIEVVPLTEEEQIEKDLQGLQEKQRLNVKRERRRKNEMKQKELQRMQMNMITPTDIGIEAASLGKESLFNLKTAEKTGILNDLAKGKKRMIFTDDELAKDNDIYIDENIMIKDKDSAADADDLESELNAMYSDYKTRRSERDAKFRAKQARGGDNEEEWTGFNEGSLEKKEEEGKDYIEDNDDEGVEGDSDDDEAITNLISKLKGQEGDHKLSSKARMIFNDPIFNNVEPDLPVNTVNDGIMSSESVGDISKLNKKRKHEEMHQKQDEADSSDESSSDDSDFEIVANDNASEEFDSDYDSEEEKNQTKKEKHSRDIDIATVEAMTLAHQLALGQKNKHDLVDEGFNRYTFRDTENLPDWFLEDEKEHSKINKPITKEAAMAIKEKIKAMNARPIKKVAEAKARKRMRAVARLEKIKKKAGLINDDSDKTEKDKAEEISRLMRKVTKKPKTKPKVTLVVASGRNKGLAGRPKGVKGKYKMVDGVMKNEQRALRRIAKKHHKKK

Entity 25 Entity 25 polymer

Description description	60S ribosomal protein L37-A
Molecular weight formula_weight	9877.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	j

MGKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA

Entity 26 Entity 26 polymer

Description description	SPB4 isoform 1
Molecular weight formula_weight	69492.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	x

MSKSLEWDNLGFSLLPWIRTGLDVMGFETMTPVQASTIPMLAGNKDVVVDSVTGSGKTAAFVIPVLEKVVKEEANTSKFKKAHFHSLIIAPTRELSRQIESVVLSFLEHYPSDLFPIKCQLLVGTNEATVRDDVSNFLRNRPQILIGTPGRVLDFLQMPAVKTSACSMVVMDEADRLLDMSFIKDTEKILRLLPKQRRTGLFSATMRSAGSDIFKTGLRNPVRITVNSKNQAPSSLKLNYCVVNPAEKLQLLVSILNNYKFKKCIVYFPTCVSVSYFYSFIQYLGKRNILVNEVEIFSLHGKLQTSARTKTLTAFTDSLSNSVLFTTDVAARGIDIPDVDLVIQLDPPTNTDMFMHRCGRTGRANRVGKAITFLNEGREEDFIPFMQVKNVELEELDLEVKGITANFYEDFRNWILEDRDRFDKGVKAYVAFIKYYSNHSATSIFRLQSLDYVGIAKLYGLFRLPRMPEITKYLATEKQEGIFPGNWLVDPPVNMDEYKYKDKKREKERQETLKNISLINDKKKLKSELKKKNLAWSDKTLTKERKLERKEKMSLKRKAIEEELKAEELDENAEEERIKEDWKEIVLQNKRKKVSSKAIQGNFDDL

Entity 27 Entity 27 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7nadR01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1650 — 50s Ribosomal Protein L19e, Chain O, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7nadw01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12760 —

Domain ID domain_id	7nadx01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7nadx02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

▶

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	3.04 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	198000

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model

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

RRP17 isoform 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NOC2 isoform 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

60S ribosomal protein L3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RPL8A isoform 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NOC3 isoform 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

60S ribosomal protein L17-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

60S ribosomal protein L19-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

60S ribosomal protein L22-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

60S ribosomal protein L25

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

60S ribosomal protein L27-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer