SAXSdb — 487d

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

50S ribosomal protein L1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL1_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–224； UniProt 6–229

50S ribosomal protein L2

OrganismNot specified

UniProt P04257

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL2_GEOSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–135； UniProt 61–195

50S ribosomal protein L6

OrganismNot specified

UniProt P02391

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL6_GEOSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain J； PDBConstruct 1–164； UniProt 8–171

50S ribosomal protein L9

OrganismNot specified

UniProt P02417

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL9_GEOSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain K； PDBConstruct 1–149； UniProt 1–149

50S ribosomal protein L11

OrganismNot specified

UniProt P29395

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL11_THEMA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain L； PDBConstruct 1–133； UniProt 8–140

50S ribosomal protein L14

OrganismNot specified

UniProt P04450

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L25 × 1 （C3T3H7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL14_GEOSE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 1–122； UniProt 1–122

50S ribosomal protein L25

OrganismNot specified

UniProt C3T3H7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3T3H7_ECOLX
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain N； PDBConstruct 1–94； UniProt 1–94

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	487d
Deposition date deposition_date	2000-02-23
Structure title title	SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION
Keywords keywords	;RIBOSOME, LARGE RIBOSOMAL SUBUNIT, RIBOSOMAL PROTEIN, PROTEIN BIOSYNTHESIS, EM-RECONSTRUCTION, ATOMIC STRUCTURE, 3D ARRANGEMENT, FITTING ;; 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.

487d__assembly_1__model_1

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

Download this curve (.dat)

487d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

487d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	95.46 Å
Rg (electron density)	95.86 Å
Total Rg	95.85 Å
Atom count	8778
Residues	1018
Excluded volume	140930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`487d__assembly_1__model_1`	heptameric （7）	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 (7)

Entity 1 Entity 1 polymer

Description description	50S ribosomal protein L1
Molecular weight formula_weight	24331.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	8778

KRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L2
Molecular weight formula_weight	14759.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRMILGKCRATVGEV

Entity 3 Entity 3 polymer

Description description	50S ribosomal protein L6
Molecular weight formula_weight	17811.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

PIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHHRALHGTTRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGLEIEVPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKGKGIRYEGELVRL

Entity 4 Entity 4 polymer

Description description	50S ribosomal protein L9
Molecular weight formula_weight	16341.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAEELANAKKLKEQLEKLTVTIPAKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALGYTNVPVKLHPEVTATLKVHVTEQK

Entity 5 Entity 5 polymer

Description description	50S ribosomal protein L11
Molecular weight formula_weight	14294.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV

Entity 6 Entity 6 polymer

Description description	50S ribosomal protein L14
Molecular weight formula_weight	13369.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MIQQESRLKVADNSGAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVKKGQVVKAVVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELRDKDFMKIISLAPEVI

Entity 7 Entity 7 polymer

Description description	50S ribosomal protein L25
Molecular weight formula_weight	10713.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d487dh_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487di_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dj_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dk_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dl_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dm_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dn_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

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7. Citations (9)

;The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution. ;

J.Mol.Biol. (2000)

PMID: 10756104 · DOI: 10.1006/jmbi.2000.3635 PRIMARY

A Detailed View of a Ribosomal Active Site: The Structure of the Gtpase Center at 2.6 Angstroms Resolution.

Cell(Cambridge,Mass.) (1999)

DOI: 10.1016/S0092-8674(00)80759-X

The NMR Structure of the 5S Rrna E-Domain-Protein C25 Complex Shows Pre-Formed and Induced Recognition.

Embo J. (1999)

DOI: 10.1093/emboj/18.22.6508

;The Three-Dimensional Structure of the RNA-Binding Domain of Ribosomal Protein L2; a Protein at the Peptidyl Transferase Center of the Ribosome. ;

Embo J. (1999)

DOI: 10.1093/emboj/18.6.1459

The Escherichia coli large ribosomal subunit at 7.5 A resolution

Structure (1999)

DOI: 10.1016/S0969-2126(00)88348-3

Ribosomal Protein L9: A Structure Determination by the Combined Use of X-Ray Crystallography and NMR Spectroscopy.

J.Mol.Biol. (1996)

DOI: 10.1006/jmbi.1996.0696

Crystal Structure of the RNA Binding Ribosomal Protein L1 from Thermus Thermophilus.

Embo J. (1996)

The Crystal Structure of Ribosomal Protein L14 Reveals an Important Organizational Component of the Translational Apparatus.

Structure (1996)

DOI: 10.1016/S0969-2126(96)00115-3

Ribosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA Binding Proetin.

Embo J. (1993)

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	1

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

Resolution resolution	7.500 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	7.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	16000

SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION

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

50S ribosomal protein L1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L11

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L14

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

487d__assembly_1__model_1

487d__assembly_1__model_1 | I(q)

487d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer