7naf

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model

Method: ELECTRON MICROSCOPY

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

Nucleolar complex protein 2

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 60S ribosomal protein L23-A × 1 （P0CX41） Ribosome biogenesis protein RLP24 × 1 （Q07915） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） UPF0642 protein YBL028C × 1 （P38202） Nuclear GTP-binding protein NUG1 × 1 （P40010） Eukaryotic translation initiation factor 6 × 1 （Q12522） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOC2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 8； PDBConstruct 1–39； UniProt 3–41

60S ribosomal protein L23-A

OrganismNot specified

UniProt P0CX41

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） Ribosome biogenesis protein RLP24 × 1 （Q07915） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） UPF0642 protein YBL028C × 1 （P38202） Nuclear GTP-binding protein NUG1 × 1 （P40010） Eukaryotic translation initiation factor 6 × 1 （Q12522） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL23A_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain V； PDBConstruct 1–134； UniProt 4–137

Ribosome biogenesis protein RLP24

OrganismNot specified

UniProt Q07915

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） 60S ribosomal protein L23-A × 1 （P0CX41） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） UPF0642 protein YBL028C × 1 （P38202） Nuclear GTP-binding protein NUG1 × 1 （P40010） Eukaryotic translation initiation factor 6 × 1 （Q12522） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RLP24_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain u； PDBConstruct 1–65； UniProt 1–65

;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ;

OrganismNot specified

UniProt P25582

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） 60S ribosomal protein L23-A × 1 （P0CX41） Ribosome biogenesis protein RLP24 × 1 （Q07915） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） UPF0642 protein YBL028C × 1 （P38202） Nuclear GTP-binding protein NUG1 × 1 （P40010） Eukaryotic translation initiation factor 6 × 1 （Q12522） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPB1_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain w； PDBConstruct 1–389； UniProt 1–389

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 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） 60S ribosomal protein L23-A × 1 （P0CX41） Ribosome biogenesis protein RLP24 × 1 （Q07915） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） UPF0642 protein YBL028C × 1 （P38202） Nuclear GTP-binding protein NUG1 × 1 （P40010） Eukaryotic translation initiation factor 6 × 1 （Q12522） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 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	8
Chains and sequence ranges	Author chain d； PDBConstruct 1–60； UniProt 13–72

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 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） 60S ribosomal protein L23-A × 1 （P0CX41） Ribosome biogenesis protein RLP24 × 1 （Q07915） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 UPF0642 protein YBL028C × 1 （P38202） Nuclear GTP-binding protein NUG1 × 1 （P40010） Eukaryotic translation initiation factor 6 × 1 （Q12522） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 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	12
Chains and sequence ranges	Author chain B； PDBConstruct 1–376； UniProt 12–387

UPF0642 protein YBL028C

OrganismNot specified

UniProt P38202

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） 60S ribosomal protein L23-A × 1 （P0CX41） Ribosome biogenesis protein RLP24 × 1 （Q07915） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） Nuclear GTP-binding protein NUG1 × 1 （P40010） Eukaryotic translation initiation factor 6 × 1 （Q12522） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBC8_YEAST
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain z； PDBConstruct 1–6； UniProt 2–7

Nuclear GTP-binding protein NUG1

OrganismNot specified

UniProt P40010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） 60S ribosomal protein L23-A × 1 （P0CX41） Ribosome biogenesis protein RLP24 × 1 （Q07915） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） UPF0642 protein YBL028C × 1 （P38202） Eukaryotic translation initiation factor 6 × 1 （Q12522） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUG1_YEAST
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain s； PDBConstruct 1–7； UniProt 1–7

Eukaryotic translation initiation factor 6

OrganismNot specified

UniProt Q12522

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） 60S ribosomal protein L23-A × 1 （P0CX41） Ribosome biogenesis protein RLP24 × 1 （Q07915） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） UPF0642 protein YBL028C × 1 （P38202） Nuclear GTP-binding protein NUG1 × 1 （P40010） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF6_YEAST
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain y； PDBConstruct 1–245； UniProt 1–245

25S rRNA (cytosine(2870)-C(5))-methyltransferase

OrganismNot specified

UniProt P40991

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 15 RNA 1	25S rRNA × 1 Ribosomal RNA-processing protein 17 × 1 Nucleolar complex protein 2 × 1 （P39744） 60S ribosomal protein L23-A × 1 （P0CX41） Ribosome biogenesis protein RLP24 × 1 （Q07915） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosome biogenesis factor Nog1 × 1 60S ribosomal protein L31-A × 1 （P0C2H8） 60S ribosomal protein L22-A × 1 60S ribosome ribosomal protein L19A × 1 60S ribosomal protein L30 × 1 60S ribosomal protein L3 × 1 （P14126） UPF0642 protein YBL028C × 1 （P38202） Nuclear GTP-binding protein NUG1 × 1 （P40010） Eukaryotic translation initiation factor 6 × 1 （Q12522） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOP2_YEAST
Isoform	—
PDB entities	16
Chains and sequence ranges	Author chain q； PDBConstruct 1–36； UniProt 285–320

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	7naf
Deposition date deposition_date	2021-06-21
Structure title title	State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local 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.

7naf__assembly_1__model_1

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

Download this curve (.dat)

7naf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7naf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.23 Å
Rg (electron density)	46.91 Å
Total Rg	47.05 Å
Atom count	18866
Residues	1715
Excluded volume	308180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7naf__assembly_1__model_1`	hexadecameric （16）	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	25S rRNA
Molecular weight formula_weight	121655.5 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	18868

AUAGGGUGAAGCCAGAGGAAACUCUGGUGGAGGCUCGAAAAUGGAAUUAGACUGAAGGUCGGCGCCCUGGAGUUAUCUUUUCUUGUUUAUCCCGCUUCGGCCCCAAGGUGAACAGCCUCUAAUGUAGAUAAGGGAAGUCGGGGGAAUCUGACUGUUAACGAGAUUCCCACUGUCCCUAUCUACUCGGGGAACUGGCUUGUCGGCUCUUCCUAUCAUACCAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGAAUUGAACUUAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGCGGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGAAUCUAUAUAUUGUAAGCUGAGAUUAAGCCU

Entity 2 Entity 2 polymer

Description description	Ribosomal RNA-processing protein 17
Molecular weight formula_weight	13077.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	5

NRQILTRGKQSKKFGTDEVTFDKDSRLDYLTGFHKRKLQRQKKAQEFIKEQERLRKIEERQKIRQERKEVMEEQLKTFKESLNLKFRYLTKNERRINQRKANDNK

Entity 3 Entity 3 polymer

Description description	Nucleolar complex protein 2
Molecular weight formula_weight	4749.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	8

KVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKT

Entity 4 Entity 4 polymer

Description description	60S ribosomal protein L23-A
Molecular weight formula_weight	14218.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

NGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMATVKKGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGKECADLWPRVASNSGVVV

Entity 5 Entity 5 polymer

Description description	Ribosome biogenesis protein RLP24
Molecular weight formula_weight	7786.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	u

MRIYQCHFCSSPCYPGHGIMFVRNDAKEFRFCRSKCHKAFKQRRNPRKLKWTKAFRKAAGKELAV

Entity 6 Entity 6 polymer

Description description	;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ;
Molecular weight formula_weight	45405.6 kDa
EC 编号 ec_number	2.1.1.167
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	w

MGKTQKKNSKGRLDRYYYLAKEKGYRARSSFKIIQINEKYGHFLEKSKVVIDLCAAPGSWCQVASKLCPVNSLIIGVDIVPMKPMPNVITFQSDITTEDCRSKLRGYMKTWKADTVLHDGAPNVGLGWVQDAFTQSQLTLQALKLAVENLVVNGTFVTKIFRSKDYNKLIWVFQQLFEKVEATKPPASRNVSAEIFVVCKGFKAPKRLDPRLLDPKEVFEELPDGQQNMESKIYNPEKKVRKRQGYEEGDNLLYHETSILDFVRTEDPISMLGEMNKFTIDENDHEWKILKKLKQTTDEFRSCIEDLKVLGKKDFKMILRWRKIAREILGIEVKDDAKTEIEVVPLTEEEQIEKDLQGLQEKQRLNVKRERRRKNEMKQKELQRMQMNM

Entity 7 Entity 7 polymer

Description description	60S ribosome biogenesis factor Nog1
Molecular weight formula_weight	8783.6 kDa
EC 编号 ec_number	2.1.1.167
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

IVLNRTQRKTPTVIRPGFKITRIRAFYMRKVKYTGEGMPEILDGKNVYIRNRQKTMIAEARNRKSLKNKAIMPR

Entity 8 Entity 8 polymer

Description description	60S ribosomal protein L31-A
Molecular weight formula_weight	7025.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

TINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRGVKGVEYRLR

Entity 9 Entity 9 polymer

Description description	60S ribosomal protein L22-A
Molecular weight formula_weight	2350.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

KYLKYLTKKYLKKNQLRD

Entity 10 Entity 10 polymer

Description description	60S ribosome ribosomal protein L19A
Molecular weight formula_weight	7490.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

KAVTVHSKRLPSQVVWIRRLRVLRRLLAKYRIDKHLYHVLYKESKGNAFKHKRALVEHIIQA

Entity 11 Entity 11 polymer

Description description	60S ribosomal protein L30
Molecular weight formula_weight	4390.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c

LGYIIIAANTPVLRKSVYYFQGGNNELGTAVGKLFRVGVVS

Entity 12 Entity 12 polymer

Description description	60S ribosomal protein L3
Molecular weight formula_weight	42452.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL

Entity 13 Entity 13 polymer

Description description	UPF0642 protein YBL028C
Molecular weight formula_weight	646.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	z

AKSLRA

Entity 14 Entity 14 polymer

Description description	Nuclear GTP-binding protein NUG1
Molecular weight formula_weight	977.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	s

MRVRKRQ

Entity 15 Entity 15 polymer

Description description	Eukaryotic translation initiation factor 6
Molecular weight formula_weight	26476.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	y

MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIGRMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPDIDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQVPLVAGTVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRLQDAQPESISGNLRDTLIETYS

Entity 16 Entity 16 polymer

Description description	25S rRNA (cytosine(2870)-C(5))-methyltransferase
Molecular weight formula_weight	3821.4 kDa
EC 编号 ec_number	2.1.1.310
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	q

LAQTLVNRGVNLQPIGSWTKVGLQIFDSQVPIGATP

Entity 17 Entity 17 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 18 Entity 18 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7nafR01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	7nafd01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	440 — Ribosomal Protein L31e; Chain: W;
Homologous superfamily homologous superfamily	10 — Ribosomal protein L31

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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	3.13 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	198000

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model

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

Nucleolar complex 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

60S ribosomal protein L23-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

Ribosome biogenesis protein RLP24

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ;

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 L31-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 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

UPF0642 protein YBL028C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nuclear GTP-binding protein NUG1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Eukaryotic translation initiation factor 6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

25S rRNA (cytosine(2870)-C(5))-methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer