6swd

IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

Method: ELECTRON MICROSCOPY

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

30S ribosomal protein S3Ae

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS3A_PYRAB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–199； UniProt 1–199

30S ribosomal protein S2

OrganismNot specified

UniProt Q9V191

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS2_PYRAB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–202； UniProt 1–202

Zn-ribbon RNA-binding protein involved in translation

OrganismNot specified

UniProt G8ZFK7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G8ZFK7_PYRAB
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–63； UniProt 1–63

30S ribosomal protein S4

OrganismNot specified

UniProt P61992

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS4_PYRAB
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain D； PDBConstruct 1–180； UniProt 1–180

30S ribosomal protein S4e

OrganismNot specified

UniProt Q9V1U8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS4E_PYRAB
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain E； PDBConstruct 1–243； UniProt 1–243

30S ribosomal protein S5

OrganismNot specified

UniProt Q9V1V5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS5_PYRAB
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain F； PDBConstruct 1–236； UniProt 1–236

30S ribosomal protein S6e

OrganismNot specified

UniProt Q9UYS3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS6E_PYRAB
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain G； PDBConstruct 1–125； UniProt 1–125

30S ribosomal protein S8

OrganismNot specified

UniProt Q9V1V0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS8_PYRAB
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–130； UniProt 1–130

30S ribosomal protein S8e

OrganismNot specified

UniProt Q9UZL4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS8E_PYRAB
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 1–127； UniProt 1–127

30S ribosomal protein S11

OrganismNot specified

UniProt P62010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS11_PYRAB
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain M； PDBConstruct 1–137； UniProt 1–137

30S ribosomal protein S12

OrganismNot specified

UniProt P61994

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS12_PYRAB
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain N； PDBConstruct 1–147； UniProt 1–147

30S ribosomal protein S15

OrganismNot specified

UniProt Q9V2K9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS15_PYRAB
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain Q； PDBConstruct 1–158； UniProt 1–158

30S ribosomal protein S17

OrganismNot specified

UniProt Q9V1U5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS17_PYRAB
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain R； PDBConstruct 1–113； UniProt 1–113

30S ribosomal protein S24e

OrganismNot specified

UniProt Q9UY20

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS24_PYRAB
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain V； PDBConstruct 1–99； UniProt 1–99

30S ribosomal protein S27e

OrganismNot specified

UniProt Q9UXZ3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein aL41 × 1 mRNA × 1 Translation initiation factor 1A × 1 （Q9V138） MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS27_PYRAB
Isoform	—
PDB entities	16
Chains and sequence ranges	Author chain W； PDBConstruct 1–65； UniProt 1–65

Translation initiation factor 1A

Pyrococcus abyssi (strain GE5 / Orsay)

UniProt Q9V138

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 17 RNA 2	16S ribosomal RNA × 1 30S ribosomal protein S3Ae × 1 （Q9V2K7） 30S ribosomal protein S2 × 1 （Q9V191） Zn-ribbon RNA-binding protein involved in translation × 1 （G8ZFK7） 30S ribosomal protein S4 × 1 （P61992） 30S ribosomal protein S4e × 1 （Q9V1U8） 30S ribosomal protein S5 × 1 （Q9V1V5） 30S ribosomal protein S6e × 1 （Q9UYS3） 30S ribosomal protein S8 × 1 （Q9V1V0） 30S ribosomal protein S8e × 1 （Q9UZL4） 30S ribosomal protein S11 × 1 （P62010） 30S ribosomal protein S12 × 1 （P61994） 30S ribosomal protein S15 × 1 （Q9V2K9） 30S ribosomal protein S17 × 1 （Q9V1U5） 30S ribosomal protein S24e × 1 （Q9UY20） 30S ribosomal protein S27e × 1 （Q9UXZ3） 30S ribosomal protein aL41 × 1 mRNA × 1 MAGNESIUM ION × 25 ZINC ION × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF1A_PYRAB
Isoform	—
PDB entities	19
Chains and sequence ranges	Author chain 6； PDBConstruct 1–113； UniProt 1–113

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	6swd
Deposition date deposition_date	2019-09-20
Structure title title	IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Keywords keywords	Translation initiation, cryo-EM, ribosome, tRNA, evolution, archaea, rRNA modifications; 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.

6swd__assembly_1__model_1

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

Download this curve (.dat)

6swd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6swd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	58.12 Å
Rg (electron density)	59.50 Å
Total Rg	59.46 Å
Atom count	41522
Residues	3325
Excluded volume	658160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6swd__assembly_1__model_1`	nonadecameric （19）	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 (22)

Entity 1 Entity 1 polymer

Description description	16S ribosomal RNA
Molecular weight formula_weight	340430.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	2
Atom count atom_count	41548

AUUCNGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCNGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCNGAAGAUCGGUACGGGCNGUGAGAGCGGGAGCCNGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCNGCAAUGCGGGAAACNGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCNGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCNGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCNGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACNGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACNGGGAGAGGCNGGGGGUACCCCNGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCNGGCUGGAACGGGUCNGACGGUGAGGGCNGAAGGCCAGGGGAGCGAACNGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCNGUAGGGAAGCNGUUAAGCCNGCNGCCUGGGGAGUACGGCNGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCCUGCUCCUUGCACACACCGCCXGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCNGUAGGGGAACCUACGGCUCGAUCACCUCCU

Entity 2 Entity 2 polymer

Description description	30S ribosomal protein S3Ae
Molecular weight formula_weight	22888.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MAAKRRVSAAKDKWKLKQWYVIYAPDFFGGVEVGLTPADDPEKVLNRVVEVTLKDITGDFLKGHVKLYFQVYDVKGQNAYTKFKGMKLARSYIRSLVRRRTTRIDGIFNITTKDGYKLRVMAMVIAARRIQTSQERAIRKIMQEIIYKKAEELNFKDFVLEAVNGKIAAEIAKEAKKIYPLKKAEIRKIKVLGEPEVAA

Entity 3 Entity 3 polymer

Description description	30S ribosomal protein S2
Molecular weight formula_weight	23026.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MADEYLVPLDQYLAAGVHIGTQQKTKDMKKFIYRVRQDGLYVLDVRKTDERLKVAGKFLARFDPQSILAVSVRLYGQKPVKKFGEVTGARAIPGRFLPGTMTNPAVKNFFEPDVIIITDPRADHQAMKEAIEIGIPIVALVDTENLLSYVDLAIPTNNKGRKALALIYWILAREILYNRGEISSREEFKIPVEEFEMKIVRR

Entity 4 Entity 4 polymer

Description description	Zn-ribbon RNA-binding protein involved in translation
Molecular weight formula_weight	7163.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAENVELKFEIPVCTSCGREITPREHATHFVCPNCGEAIIWRCETCRLLAKPYKCPKCGWEGP

Entity 5 Entity 5 polymer

Description description	30S ribosomal protein S4
Molecular weight formula_weight	21381.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGDPKRQRKKYETPPHPWIKERLDRERVLMDKYELKNKKELWKHETQLKNFRRRARRLLAARGKQAEIEREQLLARLKRLGLLPEDAVLDDVLSLTIEDILERRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTSPFANPQHPERMMIEKAKQGGEA

Entity 6 Entity 6 polymer

Description description	30S ribosomal protein S4e
Molecular weight formula_weight	28246.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MARKGPKRHLKRLAAPTSWYIERKAYKWAVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEEEANIKPLRIRNKRMVKGAKIQLNFHDGTNHLIPLSEKDNYFTSYTVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKKFPMGWPDVVTIEDEEGELFDTLKEYAFVVGRDKPRISLP

Entity 7 Entity 7 polymer

Description description	30S ribosomal protein S5
Molecular weight formula_weight	26523.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSQEWKEYAKRVLDEWQPKTKLGMLVKEGQITDIHEIFRKGYQIKEPEIIDVLLPEVNARENQEILDIALTVRMTDSGRRVRFRVLAAVGNRDGYVGLGIGHGREVGIAIRKAINYAKLNIIEIKRGCGSWECRCRRPHSVPFTVEGKEGSVRVKLIPGPRGLGLVIGDVGKKILRLAGIQDVWSQTLGETRTTVNFAKAVFNALYNTNKVVVTPEMIERYGIVVGRAMPASFTLE

Entity 8 Entity 8 polymer

Description description	30S ribosomal protein S6e
Molecular weight formula_weight	14029.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MATFKLVISDPKTGIAKQIEITGPEAEKLIGKRIGDQIPVKELGINLNELFGKEFPEDVKMEIRGGTDKDGFPMRPDIHGPRRVRILLSKGPGFRPKEKGERRKKTVRGNTISPEIVQVNVKLVY

Entity 9 Entity 9 polymer

Description description	30S ribosomal protein S8
Molecular weight formula_weight	14772.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MTLLDPLANALSHITNSERVGKREVYIKPASKLIGEVLRVMQKYGYIGEFEFIDDGRAGVYRVQLLGKINKAGAIKPRFPVKARDYERWEKRFLPAFEFGILIVSTSQGVMSHKEAREKGIGGRLIAYVY

Entity 10 Entity 10 polymer

Description description	30S ribosomal protein S8e
Molecular weight formula_weight	14293.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MAIWQGRSLRKPSGGRIVLARKKRKRELGREPSNTRVAEQDKRKIIRTYGGNKKVRLTAAAYANVFDKSGKGRKVRIIRVIENPANRQFARRNIITKGAIIETEIGKAKVTSRPGQDGVVNAILLEE

Entity 11 Entity 11 polymer

Description description	30S ribosomal protein S11
Molecular weight formula_weight	14773.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MSEEQVNIKKKEKWGIAHIYSSYNNTIIHITDITGAETISRWSGGMVVKADRDEPSPYAAMLAARRAAEEALEKGIVGVHIRVRAPGGSKSKTPGPGAQAAIRALARAGLKIGRVEDVTPIPHDGTRPKGGRRGRRV

Entity 12 Entity 12 polymer

Description description	30S ribosomal protein S12
Molecular weight formula_weight	16477.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MPGKKAPNGEFAGRKLKLKRKKFRWSDIRYKRRVLRLKEKSDPLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVVTAFCPGDGAIKFIDEHDEVIIEGIGGPKGGSMGDIPGIRYKVVKVNRVSLKELVKGRKEKPRR

Entity 13 Entity 13 polymer

Description description	30S ribosomal protein S15
Molecular weight formula_weight	18697.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

MARMHARKRGKSGSKRPPRTAPPIWLEYTVEDIENLVVKLRKEGYSTAMIGTILRDQYGIPTVKLFRDPDNPNRKLTITRILEKHGLAPEIPEDLMFLIKRAVNLRKHLEQHPKDLHSMRGLQLIESKIRRLVKYYKRKGKLPKDWRYDPEQAKLLVR

Entity 14 Entity 14 polymer

Description description	30S ribosomal protein S17
Molecular weight formula_weight	13364.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MVRDIGLRIQPPAEKCDDPKCPWHGHLKIHGRVFEGIVVSDKPRKTVTVERQYYHYLKKYERYELRRSRIHAHNPPCINAKVGDRVLIAETRPLSKTKHFVVVAVLERAEERR

Entity 15 Entity 15 polymer

Description description	30S ribosomal protein S24e
Molecular weight formula_weight	11798.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

MEIKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQYIRSYFGSYKSKGYAKYYYDKDRMLYIEPEYILIRDGIIEKKEGE

Entity 16 Entity 16 polymer

Description description	30S ribosomal protein S27e
Molecular weight formula_weight	7186.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

MALPRNVIPMPRSRFLRVKCIDCGNEQIVFSHPATRVRCNVCGATLVEPTGGKGIIRAKILEVLE

Entity 17 Entity 17 polymer

Description description	30S ribosomal protein aL41
Molecular weight formula_weight	4910.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0

MKRRPRKWKKKGRMRWKWIKKRIRRLKRQRKKERGL

Entity 18 Entity 18 polymer

Description description	mRNA
Molecular weight formula_weight	6448.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	5

UGGAGGUGAUUUAAAUGCCA

Entity 19 Entity 19 polymer

Description description	Translation initiation factor 1A
Molecular weight formula_weight	13078.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	6

MPKKERKVEGDEVIRVPLPEGNQLFGVVEQALGAGWMDVRCEDGKIRRCRIPGKLRRRVWIRVGDLVIVQPWPVQSDKRGDIVYRYTQTQVDWLLRKGKITQEFLTGGSLLVE

Source Source

Source organism organism	Pyrococcus abyssi (strain GE5 / Orsay)
NCBI taxonomy ID ncbi_taxonomy_id	272844
Host organism host_organism	Escherichia coli

Entity 20 Entity 20 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	25

Entity 21 Entity 21 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 22 Entity 22 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

▼

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	6swd600
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	6swdB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	6swdF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6swdI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6swdI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6swdM00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	80 — Ribosomal protein S11/S14

Domain ID domain_id	6swdQ02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	10 — S15/NS1, RNA-binding

Domain ID domain_id	6swdV00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	6swdW00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	100 — Ribosomal protein S27

▶

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	—

Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	142000

IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

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

30S ribosomal protein S3Ae

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Zn-ribbon RNA-binding protein involved in translation

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S4e

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S6e

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S8e

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S11

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer