SAXSdb — 5aff

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

SYMPORTIN 1

CHAETOMIUM THERMOPHILUM

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 24–676	Not recorded	RIBOSOMAL PROTEIN L5 × 1 （G0SEG2） RIBOSOMAL PROTEIN L11 × 1 （G0SHQ2）	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M SODIUM ACETATE, 8% (V/V) PEG 4000	Resolution 3.40 Å R-free 0.300

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 5AFF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GMN Structural basis of Rpl5 recognition by Syo1 Deposited 2012-08-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–676（676 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M succinic acid pH 7.0, 20% (v/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.95 Å R-free 0.259
4GMO Crystal structure of Syo1 Deposited 2012-08-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–676（676 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；0.2 M potassium acetate, 20% (v/v) PEG 3350, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.10 Å R-free 0.256
7OZS Structure of the hexameric 5S RNP from C. thermophilum Deposited 2021-06-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain F 1–676（676 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G0S5S6_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–654； UniProt 24–676

RIBOSOMAL PROTEIN L5

CHAETOMIUM THERMOPHILUM

UniProt G0SEG2

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–41	Fragment：N-TERMINUS LINEAR MOTIF, UNP RESIDUES 1-41	SYMPORTIN 1 × 1 （G0S5S6） RIBOSOMAL PROTEIN L11 × 1 （G0SHQ2）	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M SODIUM ACETATE, 8% (V/V) PEG 4000	Resolution 3.40 Å R-free 0.300

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 5AFF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GMN Structural basis of Rpl5 recognition by Syo1 Deposited 2012-08-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–45（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M succinic acid pH 7.0, 20% (v/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.95 Å R-free 0.259
7OLC Thermophilic eukaryotic 80S ribosome at idle POST state Deposited 2021-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric	Chain LD 1–304（304 aa）	Not recorded	MG MAGNESIUM ION × 571 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7OLD Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state Deposited 2021-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric	Chain LD 1–304（304 aa）	Not recorded	MG MAGNESIUM ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7OZS Structure of the hexameric 5S RNP from C. thermophilum Deposited 2021-06-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain A 1–304（304 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7Z3N Cryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-1 conformation Deposited 2022-03-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 86-meric	Chain LD 1–304（304 aa）	Not recorded	MG MAGNESIUM ION × 455 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7Z3O Cryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-2 conformation Deposited 2022-03-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 86-meric	Chain LD 1–304（304 aa）	Not recorded	MG MAGNESIUM ION × 472 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8I9R Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP Deposited 2023-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain LD 1–304（304 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8OO0 Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome Deposited 2023-04-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric	Chain LD 1–304（304 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8PV1 Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.56 Å
8PV2 Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
8PV3 Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8PV4 Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8PV5 Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
8PV6 Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 64-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8PV7 Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.12 Å
8PV8 Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
8PVK Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
8PVL Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric	Chain LD 1–304（304 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.19 Å
9I1W High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum Deposited 2025-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric	Chain LD 1–304（304 aa）	Not recorded	SPD SPERMIDINE × 2 SPM SPERMINE × 2 MG MAGNESIUM ION × 239 K POTASSIUM ION × 188 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.38 Å
9I78 Cryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon Deposited 2025-01-31	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 LD 1–304（304 aa）	Not recorded	MG MAGNESIUM ION × 379	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；waiting time: 15 s blot force: 0	Resolution 2.20 Å

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G0SEG2_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 8–48； UniProt 1–41

RIBOSOMAL PROTEIN L11

CHAETOMIUM THERMOPHILUM

UniProt G0SHQ2

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–173	Not recorded	SYMPORTIN 1 × 1 （G0S5S6） RIBOSOMAL PROTEIN L5 × 1 （G0SEG2）	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M SODIUM ACETATE, 8% (V/V) PEG 4000	Resolution 3.40 Å R-free 0.300

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 5AFF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7OLC Thermophilic eukaryotic 80S ribosome at idle POST state Deposited 2021-05-19	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric	Chain LJ 1–173（173 aa）	Not recorded	MG MAGNESIUM ION × 571 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7OLD Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state Deposited 2021-05-19	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric	Chain LJ 1–173（173 aa）	Not recorded	MG MAGNESIUM ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7OZS Structure of the hexameric 5S RNP from C. thermophilum Deposited 2021-06-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain B 1–173（173 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7Z3N Cryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-1 conformation Deposited 2022-03-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 86-meric	Chain LJ 1–173（173 aa）	Not recorded	MG MAGNESIUM ION × 455 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7Z3O Cryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-2 conformation Deposited 2022-03-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 86-meric	Chain LJ 1–173（173 aa）	Not recorded	MG MAGNESIUM ION × 472 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8I9R Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP Deposited 2023-02-07	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 LJ 1–173（173 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8OO0 Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome Deposited 2023-04-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric	Chain LJ 1–173（173 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8PV1 Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite structure Deposited 2023-07-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.56 Å
8PV2 Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 Deposited 2023-07-17	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 LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
8PV3 Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - composite structure Deposited 2023-07-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8PV4 Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure Deposited 2023-07-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric	Chain LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8PV5 Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - composite structure Deposited 2023-07-17	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 LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
8PV6 Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure Deposited 2023-07-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 64-meric	Chain LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8PV7 Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure Deposited 2023-07-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.12 Å
8PV8 Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure Deposited 2023-07-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric	Chain LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
8PVK Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - composite structure Deposited 2023-07-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric	Chain LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
8PVL Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure Deposited 2023-07-17	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: 58-meric	Chain LJ 1–173（173 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.19 Å
9I1W High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum Deposited 2025-01-17	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: 51-meric	Chain LJ 1–173（173 aa）	Not recorded	SPD SPERMIDINE × 2 SPM SPERMINE × 2 MG MAGNESIUM ION × 239 K POTASSIUM ION × 188 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.38 Å
9I78 Cryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon Deposited 2025-01-31	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 LJ 1–173（173 aa）	Not recorded	MG MAGNESIUM ION × 379	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；waiting time: 15 s blot force: 0	Resolution 2.20 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G0SHQ2_CHATD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–173； UniProt 1–173

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	5aff
Deposition date deposition_date	2015-01-21
Structure title title	Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site
Keywords keywords	CHAPERONE, RIBOSOME BIOGENESIS, ALPHA SOLENOID.; CHAPERONE
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	31.75 Å
Radius of gyration Rg (electron density) rg_electron	31.30 Å
Forward intensity I(0) i0	97221700.00
Molecular weight molecular_weight	79570.0 kDa
Excluded volume excluded_volume	100390 Å³
Envelope volume envelope_volume	131160 Å³
Hydration-shell volume shell_volume	36092 Å³
Envelope diameter envelope_diameter	108.4 Å
Shell Rg shell_rg	37.10 Å
Envelope Rg envelope_rg	31.44 Å
Shape Rg shape_rg	31.28 Å
Total Rg total_rg	31.91 Å
Total atoms total_atoms	5606
Residues n_residues	712
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	103.2 Å
Rg (real space) rg_real	31.82 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	9.7220e+07
I(0) uncertainty (real space) i0_real_error	1.6120e+06
Rg (reciprocal space) rg_reciprocal	31.79 Å
I(0) (reciprocal space) i0_reciprocal	97220000.0000
Solution quality estimate total_estimate	0.8887
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.0 Å
Skewness Skewness skewness	0.369
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	32870000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.825

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SYMPORTIN 1
Molecular weight formula_weight	72162.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5606

MTDPELAKLREDKILPVLKDLKSPDAKSRTTAAGAIANIVQDAKCRKLLLREQVVHIVLTETLTDNNIDSRAAGWEILKVLAQEEEADFCVHLYRLDVLTAIEHAAKAVLETLTTSEPPFSKLLKAQQRLVWDITGSLLVLIGLLALARDEIHEAVATKQTILRLLFRLISADIAPQDIYEEAISCLTTLSEDNLKVGQAITDDQETHVYDVLLKLATGTDPRAVMACGVLHNVFTSLQWMDHSPGKDGACDAILIPTLTRALEHVVPGGAKFNGDARYANITLLALVTLASIGTDFQETLVKGNQGSRESPISAADEEWNGFDDADGDAMDVDQKSSSGEDQEEDYEEIDVKEDDEDDDDDSITSEMQADMERVVGADGTDDGDLEDLPTLRELIQTAVPQLIRLSNLPIDSDESLTIQSHALSALNNISWTISCLEFANGENANIHNAWYPTAKKIWRKTILPILEADSADLKLATQVTSLAWAVARVLHGETPTDGNPHRKFISLYHSSKQQAGGNSNSIEEPEDPFQGLGVKCIGVVGSLAHDPAPIEVNREVGVFLVTLLRQSNNVPPAEIVEALNQLFDIYGDEELACDKEVFWKDGFLKHLEEFLPKMRTLTKGIDKRTQPELRTRADEALLNLGRFVQYKKKHAPK

来源 Source

来源生物 organism	CHAETOMIUM THERMOPHILUM
NCBI Class编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	RIBOSOMAL PROTEIN L5
Molecular weight formula_weight	6060.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHHHHHHMAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAK

来源 Source

来源生物 organism	CHAETOMIUM THERMOPHILUM
NCBI Class编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	RIBOSOMAL PROTEIN L11
Molecular weight formula_weight	20119.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSSEKAQNPMRELRIQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVYSKARYTVRQFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYELRRRNFSETGNFGFGISEHIDLGIKYDPSIGIYGMDFYCCMTRPGERVAKRRRCKSRIGASHRITREETIRWFKQRFDGIVR

来源 Source

来源生物 organism	CHAETOMIUM THERMOPHILUM
NCBI Class编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	ESCHERICHIA COLI

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5affA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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8. Citations (1)

▶

Unit-cell length a length_a	60.087 Å
Unit-cell length b length_b	105.959 Å
Unit-cell length c length_c	147.234 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.398 Å
Low-resolution limit resolution_low	49.256 Å
R factor r_factor	0.2391
R_work r_work	0.2361
R_free r_free	0.2998

fit	/app/data/saxs_computation/af/5aff/5aff.fit
pddf	/app/data/pr_computation/af/5aff/5aff.pr.out
profile	/app/data/saxs_computation/af/5aff/5aff.dat

Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site

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

SYMPORTIN 1

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L5

State in the Current Structure

Other States of the Same Protein in the Database

RIBOSOMAL PROTEIN L11

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)