SAXSdb — 6ji2

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

Elongation factor 1-alpha

Aeropyrum pernix K1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Protein pelota homolog × 1 （Q9YAZ5） Archaeal ribosomal stalk protein aP1 × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SODIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein pelota homolog × 1 （Q9YAZ5） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EF1A_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–440； UniProt 1–437 Author chain E； PDBConstruct 4–440； UniProt 1–437

Protein pelota homolog

Aeropyrum pernix K1

UniProt Q9YAZ5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Elongation factor 1-alpha × 1 （Q9YAV0） Archaeal ribosomal stalk protein aP1 × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SODIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Elongation factor 1-alpha × 1 （Q9YAV0） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PELO_AERPE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 21–376； UniProt 1–356 Author chain F； PDBConstruct 21–376； UniProt 1–356

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	6ji2
Deposition date deposition_date	2019-02-20
Structure title title	Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex
Keywords keywords	translation elongation ribosomal stalk, TRANSLATION; TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

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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.

6ji2__assembly_1__model_1

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

Download this curve (.dat)

6ji2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ji2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.68 Å
Rg (electron density)	31.10 Å
Total Rg	31.64 Å
Atom count	6253
Residues	798
Excluded volume	111940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ji2__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ji2__assembly_2__model_1`	dimeric （2）	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	Elongation factor 1-alpha
Molecular weight formula_weight	49662.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	12541

GSHMAEKPHMNLVVIGHVDHGKSTLVGHLLYRLGYIEEKKLKELEEQAKSRGKESFKFAWILDKMKEERERGITIDLTFMKFETKKYVFTIIDAPGHRDFVKNMITGASQADAAILVVSARKGEFEAGMSTEGQTREHLLLARTMGIEQIIVAVNKMDAPDVNYDQKRYEFVVSVLKKFMKGLGYQVDKIPFIPVSAWKGDNLIERSPNMPWYNGPTLVEALDQLQPPAKPVDKPLRIPVQNVYSIPGAGTVPVGRVETGVLRVGDKVVFMPPGVVGEVRSIEMHYQQLQQAEPGDNIGFAVRGVSKSDIKRGDVAGHLDKPPTVAEEFEARIFVIWHPSAITVGYTPVIHVHTASVSSRIIEIKAKLDPKTGQVVEQNPQFLKAGDAAIVRFKPVKPLVVEKFSEIPQLGRFAMRDMNRTVGIGIVTDVKPAKVDIKAKLARGSGC

Source Source

Source organism organism	Aeropyrum pernix K1
NCBI taxonomy ID ncbi_taxonomy_id	272557
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein pelota homolog
Molecular weight formula_weight	41470.6 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MGSSHHHHHHSSGLVPRGSHMRVEVLDNKRRIVRLRPESEEDLWLLRITLRPGDVVRIRTSRDVPVGSGRKERVVMTLRIRLDSIEFQPFTGKLRISGIVVEGPDEFGVKGRRHSTAVSIGTWLVVERDKGWSEQELERLASGRARGTAVIAAVDYDEFALAVLAGHGMKILEDTSARLPGKDDPSREQEVEKYVDRAAKRIVEEAARHRSPIAVIAGPGQLKTSVAEKVQRAMPSLKVATVDTSMGGVAGVREALRRESVTRILRELSIVEAEGVLEEFLRRIAKSRDTVAYTPGEVLAVARMGAVDTVLLVDTLLHSPDDAVREAVDEALRLVESMGGRVIIIPGDSPAGERLVSFGGVIALLRYPVPQEARRL

Source Source

Source organism organism	Aeropyrum pernix K1
NCBI taxonomy ID ncbi_taxonomy_id	272557
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Archaeal ribosomal stalk protein aP1
Molecular weight formula_weight	1875.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

KKEEEVDLSGLSGMFGF

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6ji2A01
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

Domain ID domain_id	6ji2A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	6ji2A03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	6ji2B01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	870 — Pelota, domain A

Domain ID domain_id	6ji2B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	60 — eRF1 domain 2

Domain ID domain_id	6ji2B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

Domain ID domain_id	6ji2E01
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

Domain ID domain_id	6ji2E02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	6ji2E03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	6ji2F01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	870 — Pelota, domain A

Domain ID domain_id	6ji2F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	60 — eRF1 domain 2

Domain ID domain_id	6ji2F03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

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Unit-cell length a length_a	71.447 Å
Unit-cell length b length_b	73.405 Å
Unit-cell length c length_c	108.142 Å
Unit-cell angle α angle_alpha	98.64 °
Unit-cell angle β angle_beta	93.80 °
Unit-cell angle γ angle_gamma	100.44 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	106.420 Å
R factor r_factor	0.2031
R_work r_work	0.1991
R_free r_free	0.2792

Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex

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

Elongation factor 1-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Protein pelota homolog

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

6ji2__assembly_1__model_1

6ji2__assembly_1__model_1 | I(q)

6ji2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex

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

Elongation factor 1-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein pelota 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ji2__assembly_1__model_1

6ji2__assembly_1__model_1 | I(q)

6ji2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)