SAXSdb — 8phd

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

Cell division cycle protein 123 homolog

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Eukaryotic translation initiation factor 2 subunit 3 × 1 （P41091） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Eukaryotic translation initiation factor 2 subunit 3 × 1 （P41091） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD123_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–356； UniProt 1–336 Author chain C； PDBConstruct 21–356； UniProt 1–336

Eukaryotic translation initiation factor 2 subunit 3

Homo sapiens

UniProt P41091

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cell division cycle protein 123 homolog × 1 （O75794） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cell division cycle protein 123 homolog × 1 （O75794） ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF2G_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–111； UniProt 363–472 Author chain D； PDBConstruct 2–111； UniProt 363–472

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	8phd
Deposition date deposition_date	2023-06-19
Structure title title	Structure of Human Cdc123 bound to domain 3 of eIF2 gamma and ATP
Keywords keywords	eIF2, translation initiation, chaperone, Cdc123, ATP grasp, 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.

8phd__assembly_1__model_1

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

Download this curve (.dat)

8phd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8phd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.61 Å
Rg (electron density)	23.55 Å
Total Rg	24.45 Å
Atom count	3264
Residues	395
Excluded volume	58219 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8phd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8phd__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 (5)

Entity 1 Entity 1 polymer

Description description	Cell division cycle protein 123 homolog
Molecular weight formula_weight	41349.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6874

MGSSHHHHHHSSGLVPRGSHMKKEHVLHCQFSAWYPFFRGVTIKSVILPLPQNVKDYLLDDGTLVVSGRDDPPTHSQPDSDDEAEEIQWSDDENTATLTAPEFPEFATKVQEAINSLGGSVFPKLNWSAPRDAYWIAMNSSLKCKTLSDIFLLFKSSDFITRDFTQPFIHCTDDSPDPCIEYELVLRKWCELIPGAEFRCFVKENKLIGISQRDYTQYYDHISKQKEEIRRCIQDFFKKHIQYKFLDEDFVFDIYRDSRGKVWLIDFNPFGEVTDSLLFTWEELISENNLNGDFSEVDAQEQDSPAFRCTNSEVTVQPSPYLSYRLPKDFVDLSTGEDAHKLIDFLKLKRNQQEDD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Eukaryotic translation initiation factor 2 subunit 3
Molecular weight formula_weight	12349.5 kDa
EC 编号 ec_number	3.6.5.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	282

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Unit-cell length a length_a	60.462 Å
Unit-cell length b length_b	126.020 Å
Unit-cell length c length_c	74.644 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	64.220 Å
R factor r_factor	0.1788
R_work r_work	0.1764
R_free r_free	0.2048

Structure of Human Cdc123 bound to domain 3 of eIF2 gamma and ATP

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

Cell division cycle protein 123 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Eukaryotic translation initiation factor 2 subunit 3

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

8phd__assembly_1__model_1

8phd__assembly_1__model_1 | I(q)

8phd__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Structure of Human Cdc123 bound to domain 3 of eIF2 gamma and ATP

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

Cell division cycle protein 123 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

Eukaryotic translation initiation factor 2 subunit 3

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

8phd__assembly_1__model_1

8phd__assembly_1__model_1 | I(q)

8phd__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)