9hal

Pooled 50S subunit d126_(L29)-/(L22)- precursor states supplemented with Api137

Method: ELECTRON MICROSCOPY

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

Large ribosomal subunit protein uL13

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	Large ribosomal subunit protein bL17 × 1 （P0AG44） Large ribosomal subunit protein bL20 × 1 （P0A7L3） Large ribosomal subunit protein bL21 × 1 （P0AG48） 23S ribosomal RNA × 1 50S ribosomal protein L3 × 1 （P60438） Large ribosomal subunit protein uL4 × 1 （P60723） Large ribosomal subunit protein uL15 × 1 （P02413） Large ribosomal subunit protein uL24 × 1 （P60624）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL13_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain J； PDBConstruct 1–142； UniProt 1–142

Large ribosomal subunit protein bL17

OrganismNot specified

UniProt P0AG44

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	Large ribosomal subunit protein uL13 × 1 （P0AA10） Large ribosomal subunit protein bL20 × 1 （P0A7L3） Large ribosomal subunit protein bL21 × 1 （P0AG48） 23S ribosomal RNA × 1 50S ribosomal protein L3 × 1 （P60438） Large ribosomal subunit protein uL4 × 1 （P60723） Large ribosomal subunit protein uL15 × 1 （P02413） Large ribosomal subunit protein uL24 × 1 （P60624）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL17_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain N； PDBConstruct 1–120； UniProt 1–120

Large ribosomal subunit protein bL20

OrganismNot specified

UniProt P0A7L3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	Large ribosomal subunit protein uL13 × 1 （P0AA10） Large ribosomal subunit protein bL17 × 1 （P0AG44） Large ribosomal subunit protein bL21 × 1 （P0AG48） 23S ribosomal RNA × 1 50S ribosomal protein L3 × 1 （P60438） Large ribosomal subunit protein uL4 × 1 （P60723） Large ribosomal subunit protein uL15 × 1 （P02413） Large ribosomal subunit protein uL24 × 1 （P60624）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL20_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Q； PDBConstruct 1–117； UniProt 2–118

Large ribosomal subunit protein bL21

OrganismNot specified

UniProt P0AG48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	Large ribosomal subunit protein uL13 × 1 （P0AA10） Large ribosomal subunit protein bL17 × 1 （P0AG44） Large ribosomal subunit protein bL20 × 1 （P0A7L3） 23S ribosomal RNA × 1 50S ribosomal protein L3 × 1 （P60438） Large ribosomal subunit protein uL4 × 1 （P60723） Large ribosomal subunit protein uL15 × 1 （P02413） Large ribosomal subunit protein uL24 × 1 （P60624）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL21_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain R； PDBConstruct 1–103； UniProt 1–103

50S ribosomal protein L3

OrganismNot specified

UniProt P60438

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	Large ribosomal subunit protein uL13 × 1 （P0AA10） Large ribosomal subunit protein bL17 × 1 （P0AG44） Large ribosomal subunit protein bL20 × 1 （P0A7L3） Large ribosomal subunit protein bL21 × 1 （P0AG48） 23S ribosomal RNA × 1 Large ribosomal subunit protein uL4 × 1 （P60723） Large ribosomal subunit protein uL15 × 1 （P02413） Large ribosomal subunit protein uL24 × 1 （P60624）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL3_ECOLI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–209； UniProt 1–209

Large ribosomal subunit protein uL4

OrganismNot specified

UniProt P60723

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	Large ribosomal subunit protein uL13 × 1 （P0AA10） Large ribosomal subunit protein bL17 × 1 （P0AG44） Large ribosomal subunit protein bL20 × 1 （P0A7L3） Large ribosomal subunit protein bL21 × 1 （P0AG48） 23S ribosomal RNA × 1 50S ribosomal protein L3 × 1 （P60438） Large ribosomal subunit protein uL15 × 1 （P02413） Large ribosomal subunit protein uL24 × 1 （P60624）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL4_ECOLI
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain E； PDBConstruct 1–201； UniProt 1–201

Large ribosomal subunit protein uL15

OrganismNot specified

UniProt P02413

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	Large ribosomal subunit protein uL13 × 1 （P0AA10） Large ribosomal subunit protein bL17 × 1 （P0AG44） Large ribosomal subunit protein bL20 × 1 （P0A7L3） Large ribosomal subunit protein bL21 × 1 （P0AG48） 23S ribosomal RNA × 1 50S ribosomal protein L3 × 1 （P60438） Large ribosomal subunit protein uL4 × 1 （P60723） Large ribosomal subunit protein uL24 × 1 （P60624）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL15_ECOLI
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain L； PDBConstruct 1–143； UniProt 2–144

Large ribosomal subunit protein uL24

OrganismNot specified

UniProt P60624

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	Large ribosomal subunit protein uL13 × 1 （P0AA10） Large ribosomal subunit protein bL17 × 1 （P0AG44） Large ribosomal subunit protein bL20 × 1 （P0A7L3） Large ribosomal subunit protein bL21 × 1 （P0AG48） 23S ribosomal RNA × 1 50S ribosomal protein L3 × 1 （P60438） Large ribosomal subunit protein uL4 × 1 （P60723） Large ribosomal subunit protein uL15 × 1 （P02413）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL24_ECOLI
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain U； PDBConstruct 1–102； UniProt 2–103

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	9hal
Deposition date deposition_date	2024-11-04
Last revision last_revision	2025-01-22
Structure title title	Pooled 50S subunit d126_(L29)-/(L22)- precursor states supplemented with Api137
Keywords keywords	ribosome, antimicrobial peptide, RNA, ribosomal protein, PrAMP, proline-rich peptide, antibiotics, 50S, Api137; 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.

9hal__assembly_1__model_1

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

Download this curve (.dat)

9hal__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9hal__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.72 Å
Rg (electron density)	60.87 Å
Total Rg	60.95 Å
Atom count	36717
Residues	2384
Excluded volume	548480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9hal__assembly_1__model_1`	nonameric （9）	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 (9)

Entity 1 Entity 1 polymer

Description description	Large ribosomal subunit protein uL13
Molecular weight formula_weight	16050.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J
Atom count atom_count	36717

MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI

Entity 2 Entity 2 polymer

Description description	Large ribosomal subunit protein bL17
Molecular weight formula_weight	13721.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSE

Entity 3 Entity 3 polymer

Description description	Large ribosomal subunit protein bL20
Molecular weight formula_weight	13396.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

ARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA

Entity 4 Entity 4 polymer

Description description	Large ribosomal subunit protein bL21
Molecular weight formula_weight	11586.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRRKHYRKQQGHRQWFTDVKITGISA

Entity 5 Entity 5 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	941619.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A

GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUAUAAGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAGCUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUU

Entity 6 Entity 6 polymer

Description description	50S ribosomal protein L3
Molecular weight formula_weight	22277.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA

Entity 7 Entity 7 polymer

Description description	Large ribosomal subunit protein uL4
Molecular weight formula_weight	22121.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA

Entity 8 Entity 8 polymer

Description description	Large ribosomal subunit protein uL15
Molecular weight formula_weight	14877.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE

Entity 9 Entity 9 polymer

Description description	Large ribosomal subunit protein uL24
Molecular weight formula_weight	11078.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETI

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Resolution resolution	4.49 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	21282

Pooled 50S subunit d126_(L29)-/(L22)- precursor states supplemented with Api137

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

Large ribosomal subunit protein uL13

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Large ribosomal subunit protein bL17

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Large ribosomal subunit protein bL20

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Large ribosomal subunit protein bL21

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 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

Large ribosomal subunit protein uL4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Large ribosomal subunit protein uL15

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Large ribosomal subunit protein uL24

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

9hal__assembly_1__model_1

9hal__assembly_1__model_1 | I(q)

9hal__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer