7r7c

State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model

Method: ELECTRON MICROSCOPY

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

60S ribosome subunit biogenesis protein NIP7

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	25S rRNA × 1 Ribosome biogenesis protein ERB1 × 1 （A0A6V8S2P3） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） Ribosome biogenesis protein NSA2 homolog × 1 （A0A6A5PXG0） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosomal subunit assembly/export protein LOC1 × 1 （P43586） Ribosome biogenesis protein BRX1 × 1 （Q08235） rRNA-processing protein EBP2 × 1 （A0A7I9FH46） Nucleolar GTP-binding protein 1 × 1 60S ribosomal protein L1-A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIP7_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain l； PDBConstruct 1–181； UniProt 1–181

Ribosome biogenesis protein ERB1

OrganismNot specified

UniProt A0A6V8S2P3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	25S rRNA × 1 60S ribosome subunit biogenesis protein NIP7 × 1 （Q08962） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） Ribosome biogenesis protein NSA2 homolog × 1 （A0A6A5PXG0） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosomal subunit assembly/export protein LOC1 × 1 （P43586） Ribosome biogenesis protein BRX1 × 1 （Q08235） rRNA-processing protein EBP2 × 1 （A0A7I9FH46） Nucleolar GTP-binding protein 1 × 1 60S ribosomal protein L1-A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6V8S2P3_YEASX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain m； PDBConstruct 1–63； UniProt 141–203

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 10 RNA 1	25S rRNA × 1 60S ribosome subunit biogenesis protein NIP7 × 1 （Q08962） Ribosome biogenesis protein ERB1 × 1 （A0A6V8S2P3） Ribosome biogenesis protein NSA2 homolog × 1 （A0A6A5PXG0） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosomal subunit assembly/export protein LOC1 × 1 （P43586） Ribosome biogenesis protein BRX1 × 1 （Q08235） rRNA-processing protein EBP2 × 1 （A0A7I9FH46） Nucleolar GTP-binding protein 1 × 1 60S ribosomal protein L1-A × 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	4
Chains and sequence ranges	Author chain q； PDBConstruct 1–618； UniProt 1–618

Ribosome biogenesis protein NSA2 homolog

OrganismNot specified

UniProt A0A6A5PXG0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	25S rRNA × 1 60S ribosome subunit biogenesis protein NIP7 × 1 （Q08962） Ribosome biogenesis protein ERB1 × 1 （A0A6V8S2P3） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosomal subunit assembly/export protein LOC1 × 1 （P43586） Ribosome biogenesis protein BRX1 × 1 （Q08235） rRNA-processing protein EBP2 × 1 （A0A7I9FH46） Nucleolar GTP-binding protein 1 × 1 60S ribosomal protein L1-A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5PXG0_YEASX
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain r； PDBConstruct 1–103； UniProt 149–260

;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 10 RNA 1	25S rRNA × 1 60S ribosome subunit biogenesis protein NIP7 × 1 （Q08962） Ribosome biogenesis protein ERB1 × 1 （A0A6V8S2P3） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） Ribosome biogenesis protein NSA2 homolog × 1 （A0A6A5PXG0） 60S ribosomal subunit assembly/export protein LOC1 × 1 （P43586） Ribosome biogenesis protein BRX1 × 1 （Q08235） rRNA-processing protein EBP2 × 1 （A0A7I9FH46） Nucleolar GTP-binding protein 1 × 1 60S ribosomal protein L1-A × 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 1–12； UniProt 827–838

60S ribosomal subunit assembly/export protein LOC1

OrganismNot specified

UniProt P43586

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	25S rRNA × 1 60S ribosome subunit biogenesis protein NIP7 × 1 （Q08962） Ribosome biogenesis protein ERB1 × 1 （A0A6V8S2P3） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） Ribosome biogenesis protein NSA2 homolog × 1 （A0A6A5PXG0） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） Ribosome biogenesis protein BRX1 × 1 （Q08235） rRNA-processing protein EBP2 × 1 （A0A7I9FH46） Nucleolar GTP-binding protein 1 × 1 60S ribosomal protein L1-A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LOC1_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain 7； PDBConstruct 1–204； UniProt 1–204

Ribosome biogenesis protein BRX1

OrganismNot specified

UniProt Q08235

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	25S rRNA × 1 60S ribosome subunit biogenesis protein NIP7 × 1 （Q08962） Ribosome biogenesis protein ERB1 × 1 （A0A6V8S2P3） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） Ribosome biogenesis protein NSA2 homolog × 1 （A0A6A5PXG0） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosomal subunit assembly/export protein LOC1 × 1 （P43586） rRNA-processing protein EBP2 × 1 （A0A7I9FH46） Nucleolar GTP-binding protein 1 × 1 60S ribosomal protein L1-A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRX1_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain A； PDBConstruct 1–291； UniProt 1–291

rRNA-processing protein EBP2

OrganismNot specified

UniProt A0A7I9FH46

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	25S rRNA × 1 60S ribosome subunit biogenesis protein NIP7 × 1 （Q08962） Ribosome biogenesis protein ERB1 × 1 （A0A6V8S2P3） 25S rRNA (cytosine(2870)-C(5))-methyltransferase × 1 （P40991） Ribosome biogenesis protein NSA2 homolog × 1 （A0A6A5PXG0） ;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ; × 1 （P25582） 60S ribosomal subunit assembly/export protein LOC1 × 1 （P43586） Ribosome biogenesis protein BRX1 × 1 （Q08235） Nucleolar GTP-binding protein 1 × 1 60S ribosomal protein L1-A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7I9FH46_YEASX
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain J； PDBConstruct 1–96； UniProt 247–342

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	7r7c
Deposition date deposition_date	2021-06-24
Structure title title	State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk 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.

7r7c__assembly_1__model_1

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

Download this curve (.dat)

7r7c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7r7c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.25 Å
Rg (electron density)	47.61 Å
Total Rg	47.82 Å
Atom count	14950
Residues	1499
Excluded volume	250330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7r7c__assembly_1__model_1`	undecameric （11）	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 (11)

Entity 1 Entity 1 polymer

Description description	25S rRNA
Molecular weight formula_weight	72858.9 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	14950

GCGGUCGAUCGUUUCCCUCAGGAUAUUUUUGGUAAGCAGAACUACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAUAAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUAUUGUCAGGUGGGGAGUAAAGUUACCACAGGGAUAAUUGUGGCAGUCUUGCUGACCGUCGUGAGACAGGUUAG

Entity 2 Entity 2 polymer

Description description	60S ribosome subunit biogenesis protein NIP7
Molecular weight formula_weight	20411.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	l

MRQLTEEETKVVFEKLAGYIGRNISFLVDNKELPHVFRLQKDRVYYVPDHVAKLATSVARPNLMSLGICLGKFTKTGKFRLHITSLTVLAKHAKYKIWIKPNGEMPFLYGNHVLKAHVGKMSDDIPEHAGVIVFAMNDVPLGFGVSAKSTSESRNMQPTGIVAFRQADIGEYLRDEDTLFT

Entity 3 Entity 3 polymer

Description description	Ribosome biogenesis protein ERB1
Molecular weight formula_weight	6833.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	m

TQNTIGNIPLSAYDEMPHIGYDINGKRIMRPAKGSALDQLLDSIELPEGWTGLLDKNSGSSLN

Entity 4 Entity 4 polymer

Description description	25S rRNA (cytosine(2870)-C(5))-methyltransferase
Molecular weight formula_weight	69912.2 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

MGSRRHKNKQAAPPTLEEFQARKEKKANRKLEKGKRPSTTQGDEVSDRKKKKSKPFKKSRKEEEEVVEEDKDLPEVDLEELSKARKSLFDDEEDDDEAGLVDEELKDEFDLEQEYDYDEDEDNDAHPIFSDDDDEADLEELNAQNMEALSKKLDEEEAEEAEEAEMELVEAENMQPRADILPTEEQEEMMAQETPNLTSTRTRMIEIVKVLENFKTLGAEGRSRGEYVDRLLKDICEYFGYTPFLAEKLFNLFSPAEAMEFFEANEIARPITIRTNTLKTRRRDLAQTLVNRGVNLQPIGSWTKVGLQIFDSQVPIGATPEYLAGHYILQAASSFLPVIALDPHENERILDMAAAPGGKTTYISAMMKNTGCVFANDANKSRTKSLIANIHRLGCTNTIVCNYDAREFPKVIGGFDRILLDAPCSGTGVIGKDQSVKVSRTEKDFIQIPHLQKQLLLSAIDSVDCNSKHGGVIVYSTCSVAVEEDEAVIDYALRKRPNVKLVDTGLAIGKEAFTSYRGKKFHPSVKLARRYYPHTYNVDGFFVAKFQKIGPSSFDDNQASAKEKETAARKEALEEGIIHSDFATFEDEEDDKYIEKSVKNNLLKKGVNPKAKRPSNEK

Entity 5 Entity 5 polymer

Description description	Ribosome biogenesis protein NSA2 homolog
Molecular weight formula_weight	11673.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	r

RMITKHTFVGEGFTRRPVKMERIIRPSALRQKKANVTHPELGVTVFLPILAVKKNPQSPMYTQLGVLTKGTIIEVNVSELVWGKYAQVTNEPDRDGCVNAVLLD

Entity 6 Entity 6 polymer

Description description	;27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase ;
Molecular weight formula_weight	1520.8 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

QRALRRIAKKHH

Entity 7 Entity 7 polymer

Description description	60S ribosomal subunit assembly/export protein LOC1
Molecular weight formula_weight	23652.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	7

MAPKKPSKRQNLRREVAPEVFQDSQARNQLANVPHLTEKSAQRKPSKTKVKKEQSLARLYGAKKDKKGKYSEKDLNIPTLNRAIVPGVKIRRGKKGKKFIADNDTLTLNRLITTIGDKYDDIAESKLEKARRLEEIRELKRKEIERKEALKQDKLEEKKDEIKKKSSVARTIRRKNKRDMLKSEAKASESKTEGRKVKKVSFAQ

Entity 8 Entity 8 polymer

Description description	Ribosome biogenesis protein BRX1
Molecular weight formula_weight	33585.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSRKEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTMDELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFSIVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENKQYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK

Entity 9 Entity 9 polymer

Description description	rRNA-processing protein EBP2
Molecular weight formula_weight	11444.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

AFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKKAREEARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSL

Entity 10 Entity 10 polymer

Description description	Nucleolar GTP-binding protein 1
Molecular weight formula_weight	6401.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

KITRIRAFYMRKVKSLVEQVARDYVRLLKFGQSLFQCKQLKRAALGRMATIVKK

Entity 11 Entity 11 polymer

Description description	60S ribosomal protein L1-A
Molecular weight formula_weight	24538.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MSKITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLVQQILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRLY

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7r7ca01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	790 — Ribosomal protein L1/L10, domain II

Domain ID domain_id	7r7cr01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	310 —

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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	3.71 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	198000

State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model

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

60S ribosome subunit biogenesis protein NIP7

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 ERB1

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

Other homooligomers

Heteromeric or nucleic-acid complex

Ribosome biogenesis protein NSA2 homolog

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 subunit assembly/export protein LOC1

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 BRX1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

rRNA-processing protein EBP2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7r7c__assembly_1__model_1

7r7c__assembly_1__model_1 | I(q)

7r7c__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer