SAXSdb — 7zki

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

Translation initiation factor 1A

Pyrococcus abyssi GE5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 RNA 1	Met-tRNAiMet × 1 Translation initiation factor 5B × 1 （A0A3P7EHT1,Q9UZK7） METHIONINE × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1	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	2
Chains and sequence ranges	Author chain 6； PDBConstruct 22–134； UniProt 1–113

Translation initiation factor 5B

Pyrococcus abyssi GE5

UniProt A0A3P7EHT1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 RNA 1	Met-tRNAiMet × 1 Translation initiation factor 1A × 1 （Q9V138） METHIONINE × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A3P7EHT1_WUCBA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 7； PDBConstruct 1–21； UniProt 1–21

Translation initiation factor 5B

Pyrococcus abyssi GE5

UniProt Q9UZK7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 RNA 1	Met-tRNAiMet × 1 Translation initiation factor 1A × 1 （Q9V138） METHIONINE × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF2P_PYRAB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 7； PDBConstruct 22–41； UniProt 1–20 Author chain 7； PDBConstruct 42–619； UniProt 415–992

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	7zki
Deposition date deposition_date	2022-04-13
Structure title title	Cryo-EM structure of aIF1A:aIF5B:Met-tRNAiMet complex from a Pyrococcus abyssi 30S initiation complex
Keywords keywords	Initiation complex, translation initiation, small ribosomal subunit, aIF5b, TRANSLATION; TRANSLATION
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.

7zki__assembly_1__model_1

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

Download this curve (.dat)

7zki__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zki__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.70 Å
Rg (electron density)	49.38 Å
Total Rg	49.76 Å
Atom count	7120
Residues	759
Excluded volume	122020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zki__assembly_1__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	Met-tRNAiMet
Molecular weight formula_weight	24833.9 kDa
Mutation mutation	C1A, A72U
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	4
Atom count atom_count	7120

AGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCUACCA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Translation initiation factor 1A
Molecular weight formula_weight	15336.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	6

MGSSSHHHHHHSSGLVPRGSHMPKKERKVEGDEVIRVPLPEGNQLFGVVEQALGAGWMDVRCEDGKIRRCRIPGKLRRRVWIRVGDLVIVQPWPVQSDKRGDIVYRYTQTQVDWLLRKGKITQEFLTGGSLLVE

Source Source

Source organism organism	Pyrococcus abyssi GE5
NCBI taxonomy ID ncbi_taxonomy_id	272844
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Translation initiation factor 5B
Molecular weight formula_weight	69122.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	7

MGSSHHHHHHSSGLVPRGSHMMTKRIRQPIIAVLGHVDHGKTTLLDRIRKTNVAAKEAGGITQHIGATEVPIEVVKKIAGPLIKLWKAEIKLPGLLFIDTPGHEAFTSLRARGGSLADLAVLVVDINEGFQPQTIESIEILRKYRTPFVVAANKIDRIKGWVIEEDEPFLMNIKKQDQRAVQELETKLWELIGKFYEFGFQANRFDRVQNFTRELAIVPISAKYGIGIAELLVLIAGLSQRYLEEKLKIEVEGPARGTILEVREEPGLGHTIDVIIYDGTLHKDDTIVVGGKDKAIVTKIRALLKPKPLDEIRDPRFRFDYVDEVTAAAGVKIAAPGLEEALAGSPVIAAPTPEDVEKAKQEILEQIERVVISTDKVGVIVKADTLGSLEALSKELQEKEIPIRKADVGNVSKTDVMEALSVKEEEPKYGVILGFNVKVNEDAEEVAKAKDVKIFVGNVIYKLIEDYEEWVKEEEEKKKRELLSKVTFPGVIRLYPDERYVFRRSNPAIVGIEVIEGRIKPGVTLIKQNGQKVGVIRSIKSRDEFLQEAKKGQAVAIAIEGAIVGRHIHPGETLYVDLSRDDAITLLKHLRDTLEDTDIKALKMIAKVKAKEDPFWRAI

Source Source

Source organism organism	Pyrococcus abyssi GE5
NCBI taxonomy ID ncbi_taxonomy_id	272844
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	METHIONINE
Molecular weight formula_weight	149.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7zki701
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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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	—

Resolution resolution	3.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	37000

Cryo-EM structure of aIF1A:aIF5B:Met-tRNAiMet complex from a Pyrococcus abyssi 30S initiation complex

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

Translation initiation factor 1A

State in the Current Structure

Other States of the Same Protein in the Database

Translation initiation factor 5B

State in the Current Structure

Other States of the Same Protein in the Database

Translation initiation factor 5B

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7zki__assembly_1__model_1

7zki__assembly_1__model_1 | I(q)

7zki__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Cryo-EM structure of aIF1A:aIF5B:Met-tRNAiMet complex from a Pyrococcus abyssi 30S initiation complex

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

Translation initiation factor 1A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Translation initiation factor 5B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Translation initiation factor 5B

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

7zki__assembly_1__model_1

7zki__assembly_1__model_1 | I(q)

7zki__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)