8phd

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

Method: X-RAY DIFFRACTION D_max: 107.4 Å Quality: EXCELLENT

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–336	Not recorded	Eukaryotic translation initiation factor 2 subunit 3 × 1 （P41091） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG3350 0.2 M lithium citrate 1 mM ATP 5 mM MgCl2	Resolution 2.08 Å R-free 0.205
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–336	Not recorded	Eukaryotic translation initiation factor 2 subunit 3 × 1 （P41091） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG3350 0.2 M lithium citrate 1 mM ATP 5 mM MgCl2	Resolution 2.08 Å R-free 0.205

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8PHD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8PHV Structure of Human selenomethionylated Cdc123 bound to domain 3 of eIF2 gamma Deposited 2023-06-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–336（336 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG3350, 8% tacsimate	Resolution 1.97 Å R-free 0.222
8PHV Structure of Human selenomethionylated Cdc123 bound to domain 3 of eIF2 gamma Deposited 2023-06-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–336（336 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG3350, 8% tacsimate	Resolution 1.97 Å R-free 0.222

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 363–472	Not recorded	Cell division cycle protein 123 homolog × 1 （O75794） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG3350 0.2 M lithium citrate 1 mM ATP 5 mM MgCl2	Resolution 2.08 Å R-free 0.205
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 363–472	Not recorded	Cell division cycle protein 123 homolog × 1 （O75794） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG3350 0.2 M lithium citrate 1 mM ATP 5 mM MgCl2	Resolution 2.08 Å R-free 0.205

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8PHD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
28ZU human 48S PIC with Kozak mRNA and eIF1A W70A mutant Deposited 2026-03-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric	Chain E 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.20 Å
28ZV human 48S PIC with mRNA (non-Kozak) Deposited 2026-03-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric	Chain E 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.90 Å
28ZX human 48S PIC with mRNA (Kozak_1) Deposited 2026-03-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain E 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.80 Å
28ZY human 48S PIC with mRNA (Kozak_2) Deposited 2026-03-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain E 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.00 Å
6FEC Human cap-dependent 48S pre-initiation complex Deposited 2017-12-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain S 39–460（422 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Tris HCl, 50 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine 0.25 mM GMPPNP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.30 Å
6K71 eIF2 - eIF2B complex Deposited 2019-06-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain P 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
6K72 eIF2(aP) - eIF2B complex Deposited 2019-06-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain P 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6O81 Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to translation initiation factor 2 from Homo sapiens Deposited 2019-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain S 1–472（472 aa） Chain T 1–472（472 aa）	Not recorded	C7B 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
6O85 Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to eukaryotic translation initiation factor 2 from Homo sapiens Deposited 2019-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain S 1–472（472 aa）	Not recorded	C7B 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
6YBV Structure of a human 48S translational initiation complex - eIF2-TC Deposited 2020-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain t 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6ZMW Structure of a human 48S translational initiation complex Deposited 2020-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric	Chain t 1–472（472 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 89	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6ZP4 SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2 Deposited 2020-07-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric	Chain Y 1–472（472 aa）	Not recorded	ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7A09 Structure of a human ABCE1-bound 43S pre-initiation complex - State III Deposited 2020-08-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric	Chain Y 1–472（472 aa）	Not recorded	ZN ZINC ION × 4 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MET METHIONINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7D43 eIF2B-eIF2(aP), aPg complex Deposited 2020-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain P 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7F66 eIF2B-SFSV NSs-1-eIF2 Deposited 2021-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain S 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å
7F67 eIF2B-SFSV NSs-2-eIF2 Deposited 2021-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain S 1–472（472 aa） Chain T 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 Å
7QP6 Structure of the human 48S initiation complex in open state (h48S AUG open) Deposited 2022-01-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain t 1–472（472 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.	Resolution 4.70 Å
7QP7 Structure of the human 48S initiation complex in closed state (h48S AUG closed) Deposited 2022-01-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric	Chain t 1–472（472 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.	Resolution 3.70 Å
8OZ0 Structure of a human 48S translation initiation complex with eIF4F and eIF4A Deposited 2023-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric	Chain E 1–472（472 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 89	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8PHV Structure of Human selenomethionylated Cdc123 bound to domain 3 of eIF2 gamma Deposited 2023-06-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 363–472（110 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG3350, 8% tacsimate	Resolution 1.97 Å R-free 0.222
8PHV Structure of Human selenomethionylated Cdc123 bound to domain 3 of eIF2 gamma Deposited 2023-06-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 363–472（110 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG3350, 8% tacsimate	Resolution 1.97 Å R-free 0.222
8PJ1 Structure of human 48S translation initiation complex in open codon scanning state (48S-1) Deposited 2023-06-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric	Chain t 1–472（472 aa）	Not recorded	MG MAGNESIUM ION × 90 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MET METHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing	Resolution 3.40 Å
8PJ2 Structure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2) Deposited 2023-06-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain t 1–472（472 aa）	Not recorded	MG MAGNESIUM ION × 87 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing	Resolution 3.40 Å
8PJ3 Structure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3) Deposited 2023-06-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric	Chain t 1–472（472 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 89 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing	Resolution 3.70 Å
8PJ4 Structure of human 48S translation initiation complex after eIF5 release (48S-4) Deposited 2023-06-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain t 1–472（472 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 89 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing	Resolution 3.20 Å
8PPL MERS-CoV Nsp1 bound to the human 43S pre-initiation complex Deposited 2023-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric	Chain It 1–472（472 aa）	Not recorded	ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 116 MET METHIONINE × 1 UNX UNKNOWN LIGAND × 129	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.65 Å
8QZZ Crystal structure of human eIF2 alpha-gamma complexed with PPP1R15A_420-452 Deposited 2023-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–472（472 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；11-12% PEG 6000, 0.1M Tris-HCl pH8.5 supplemented with amino acids	Resolution 3.35 Å R-free 0.299
9HVE Native human eIF2-eIF2B complex Deposited 2024-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain O 1–472（472 aa） Chain P 1–472（472 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9HVF Native human PPP1R15B-P-eIF2-eIF2B complex Deposited 2024-12-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å

28 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.11 Å
Radius of gyration Rg (electron density) rg_electron	33.50 Å
Forward intensity I(0) i0	132365000.00
Molecular weight molecular_weight	93137.0 kDa
Excluded volume excluded_volume	117140 Å³
Envelope volume envelope_volume	161840 Å³
Hydration-shell volume shell_volume	40235 Å³
Envelope diameter envelope_diameter	109.0 Å
Shell Rg shell_rg	40.63 Å
Envelope Rg envelope_rg	32.31 Å
Shape Rg shape_rg	33.48 Å
Total Rg total_rg	34.20 Å
Total atoms total_atoms	6569
Residues n_residues	795
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.4 Å
Rg (real space) rg_real	34.00 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	1.3240e+08
I(0) uncertainty (real space) i0_real_error	2.0380e+06
Rg (reciprocal space) rg_reciprocal	34.07 Å
I(0) (reciprocal space) i0_reciprocal	132400000.0000
Solution quality estimate total_estimate	0.9059
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.0 Å
Skewness Skewness skewness	0.107
Kurtosis Kurtosis kurtosis	-0.693
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	52700000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.953

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/ph/8phd/8phd.fit
pddf	/app/data/pr_computation/ph/8phd/8phd.pr.out
profile	/app/data/saxs_computation/ph/8phd/8phd.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)