9y8p

Cryo-EM structure of Thermotoga maritima encapsulin shell

Method: ELECTRON MICROSCOPY D_max: 249.0 Å Quality: GOOD

▼

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

Type 1 encapsulin shell protein

Thermotoga maritima

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 homooligomer Homooligomer Protein × 60 PDB declaration: 60-meric（60） Consistent with protein copy count	Chain A； UniProt 1–265 Chain AA； UniProt 1–265 Chain AB； UniProt 1–265 Chain B； UniProt 1–265 Chain BA； UniProt 1–265 Chain BB； UniProt 1–265 Chain C； UniProt 1–265 Chain CA； UniProt 1–265 Chain CB； UniProt 1–265 Chain D； UniProt 1–265 Chain DA； UniProt 1–265 Chain DB； UniProt 1–265 Chain E； UniProt 1–265 Chain EA； UniProt 1–265 Chain EB； UniProt 1–265 Chain F； UniProt 1–265 Chain FA； UniProt 1–265 Chain FB； UniProt 1–265 Chain G； UniProt 1–265 Chain GA； UniProt 1–265 Chain GB； UniProt 1–265 Chain H； UniProt 1–265 Chain HA； UniProt 1–265 Chain HB； UniProt 1–265 Chain I； UniProt 1–265 Chain IA； UniProt 1–265 Chain J； UniProt 1–265 Chain JA； UniProt 1–265 Chain K； UniProt 1–265 Chain KA； UniProt 1–265 Chain L； UniProt 1–265 Chain LA； UniProt 1–265 Chain M； UniProt 1–265 Chain MA； UniProt 1–265 Chain N； UniProt 1–265 Chain NA； UniProt 1–265 Chain O； UniProt 1–265 Chain OA； UniProt 1–265 Chain P； UniProt 1–265 Chain PA； UniProt 1–265 Chain Q； UniProt 1–265 Chain QA； UniProt 1–265 Chain R； UniProt 1–265 Chain RA； UniProt 1–265 Chain S； UniProt 1–265 Chain SA； UniProt 1–265 Chain T； UniProt 1–265 Chain TA； UniProt 1–265 Chain U； UniProt 1–265 Chain UA； UniProt 1–265 Chain V； UniProt 1–265 Chain VA； UniProt 1–265 Chain W； UniProt 1–265 Chain WA； UniProt 1–265 Chain X； UniProt 1–265 Chain XA； UniProt 1–265 Chain Y； UniProt 1–265 Chain YA； UniProt 1–265 Chain Z； UniProt 1–265 Chain ZA； UniProt 1–265	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 Å

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 9Y8P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DKT Crystal structure of Thermotoga maritima encapsulin Deposited 2008-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 120 PDB declaration: 120-meric	Chain A 1–265（265 aa） Chain B 1–265（265 aa） Chain C 1–265（265 aa） Chain D 1–265（265 aa） Chain E 1–265（265 aa） Chain F 1–265（265 aa） Chain G 1–265（265 aa） Chain H 1–265（265 aa） Chain I 1–265（265 aa） Chain J 1–265（265 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；0.1M citrate, 21.5% MPD (v/v), 0.25M ammonium acetate, pH5.1, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.10 Å R-free 0.239
6WKV Cryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE) Deposited 2020-04-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain 0 1–265（265 aa） Chain 1 1–265（265 aa） Chain 2 1–265（265 aa） Chain 3 1–265（265 aa） Chain 4 1–265（265 aa） Chain 5 1–265（265 aa） Chain 6 1–265（265 aa） Chain 7 1–265（265 aa） Chain 8 1–265（265 aa） Chain 9 1–265（265 aa） Chain A 1–265（265 aa） Chain B 1–265（265 aa） Chain C 1–265（265 aa） Chain D 1–265（265 aa） Chain E 1–265（265 aa） Chain F 1–265（265 aa） Chain G 1–265（265 aa） Chain H 1–265（265 aa） Chain I 1–265（265 aa） Chain J 1–265（265 aa） Chain K 1–265（265 aa） Chain L 1–265（265 aa） Chain M 1–265（265 aa） Chain N 1–265（265 aa） Chain O 1–265（265 aa） Chain P 1–265（265 aa） Chain Q 1–265（265 aa） Chain R 1–265（265 aa） Chain S 1–265（265 aa） Chain T 1–265（265 aa） Chain U 1–265（265 aa） Chain V 1–265（265 aa） Chain W 1–265（265 aa） Chain X 1–265（265 aa） Chain Y 1–265（265 aa） Chain Z 1–265（265 aa） Chain a 1–265（265 aa） Chain b 1–265（265 aa） Chain c 1–265（265 aa） Chain d 1–265（265 aa） Chain e 1–265（265 aa） Chain f 1–265（265 aa） Chain g 1–265（265 aa） Chain h 1–265（265 aa） Chain i 1–265（265 aa） Chain j 1–265（265 aa） Chain k 1–265（265 aa） Chain l 1–265（265 aa） Chain m 1–265（265 aa） Chain n 1–265（265 aa） Chain o 1–265（265 aa） Chain p 1–265（265 aa） Chain q 1–265（265 aa） Chain r 1–265（265 aa） Chain s 1–265（265 aa） Chain t 1–265（265 aa） Chain u 1–265（265 aa） Chain v 1–265（265 aa） Chain w 1–265（265 aa） Chain x 1–265（265 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å
7K5W Cryo-EM structure of heterologous protein complex loaded Thermotoga maritima encapsulin capsid Deposited 2020-09-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
7K5W Cryo-EM structure of heterologous protein complex loaded Thermotoga maritima encapsulin capsid Deposited 2020-09-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
7K5W Cryo-EM structure of heterologous protein complex loaded Thermotoga maritima encapsulin capsid Deposited 2020-09-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
7K5W Cryo-EM structure of heterologous protein complex loaded Thermotoga maritima encapsulin capsid Deposited 2020-09-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
7K5W Cryo-EM structure of heterologous protein complex loaded Thermotoga maritima encapsulin capsid Deposited 2020-09-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
7KQ5 Cryo-EM structure of a thermostable encapsulin from T. maritima Deposited 2020-11-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen PROPANE；3 ul sample applied to the carbon side of the grid and blotted for 4s before plunging.	Resolution 2.00 Å
7KQ5 Cryo-EM structure of a thermostable encapsulin from T. maritima Deposited 2020-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen PROPANE；3 ul sample applied to the carbon side of the grid and blotted for 4s before plunging.	Resolution 2.00 Å
7KQ5 Cryo-EM structure of a thermostable encapsulin from T. maritima Deposited 2020-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen PROPANE；3 ul sample applied to the carbon side of the grid and blotted for 4s before plunging.	Resolution 2.00 Å
7KQ5 Cryo-EM structure of a thermostable encapsulin from T. maritima Deposited 2020-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen PROPANE；3 ul sample applied to the carbon side of the grid and blotted for 4s before plunging.	Resolution 2.00 Å
7KQ5 Cryo-EM structure of a thermostable encapsulin from T. maritima Deposited 2020-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen PROPANE；3 ul sample applied to the carbon side of the grid and blotted for 4s before plunging.	Resolution 2.00 Å
7LII Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7D Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Mutation：K182D, E183D, Del(184-190)	RBF RIBOFLAVIN × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 3.55 Å
7LII Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7D Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：K182D, E183D, Del(184-190)	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 3.55 Å
7LII Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7D Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Mutation：K182D, E183D, Del(184-190)	RBF RIBOFLAVIN × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 3.55 Å
7LII Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7D Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Mutation：K182D, E183D, Del(184-190)	RBF RIBOFLAVIN × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 3.55 Å
7LII Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7D Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：K182D, E183D, Del(184-190)	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 3.55 Å
7LIJ Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1K Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Mutation：H187K	RBF RIBOFLAVIN × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIJ Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1K Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：H187K	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIJ Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1K Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Mutation：H187K	RBF RIBOFLAVIN × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIJ Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1K Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Mutation：H187K	RBF RIBOFLAVIN × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIJ Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1K Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：H187K	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIK Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1R Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Mutation：H187R	RBF RIBOFLAVIN × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.91 Å
7LIK Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1R Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：H187R	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.91 Å
7LIK Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1R Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Mutation：H187R	RBF RIBOFLAVIN × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.91 Å
7LIK Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1R Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Mutation：H187R	RBF RIBOFLAVIN × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.91 Å
7LIK Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1R Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：H187R	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.91 Å
7LIL Thermotoga maritima Encapsulin Nanocompartment Pore Mutant SE3 Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Mutation：G186E,H187E,Y188E	RBF RIBOFLAVIN × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIL Thermotoga maritima Encapsulin Nanocompartment Pore Mutant SE3 Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：G186E,H187E,Y188E	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIL Thermotoga maritima Encapsulin Nanocompartment Pore Mutant SE3 Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Mutation：G186E,H187E,Y188E	RBF RIBOFLAVIN × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIL Thermotoga maritima Encapsulin Nanocompartment Pore Mutant SE3 Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Mutation：G186E,H187E,Y188E	RBF RIBOFLAVIN × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIL Thermotoga maritima Encapsulin Nanocompartment Pore Mutant SE3 Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：G186E,H187E,Y188E	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.84 Å
7LIM Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S6E Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Mutation：Del(184-190)	RBF RIBOFLAVIN × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.75 Å
7LIM Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S6E Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：Del(184-190)	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.75 Å
7LIM Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S6E Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Mutation：Del(184-190)	RBF RIBOFLAVIN × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.75 Å
7LIM Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S6E Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Mutation：Del(184-190)	RBF RIBOFLAVIN × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.75 Å
7LIM Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S6E Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：Del(184-190)	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 4 seconds, force 20 immediately prior to plunging into ethane	Resolution 2.75 Å
7LIS Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S5D Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Mutation：E184D,P189D, Del(185-188)	RBF RIBOFLAVIN × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.96 Å
7LIS Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S5D Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：E184D,P189D, Del(185-188)	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.96 Å
7LIS Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S5D Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Mutation：E184D,P189D, Del(185-188)	RBF RIBOFLAVIN × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.96 Å
7LIS Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S5D Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Mutation：E184D,P189D, Del(185-188)	RBF RIBOFLAVIN × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.96 Å
7LIS Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S5D Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：E184D,P189D, Del(185-188)	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.96 Å
7LIT Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–265（265 aa）	Mutation：K182G, L190G, Del(182-189)	RBF RIBOFLAVIN × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.53 Å
7LIT Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：K182G, L190G, Del(182-189)	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.53 Å
7LIT Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–265（265 aa）	Mutation：K182G, L190G, Del(182-189)	RBF RIBOFLAVIN × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.53 Å
7LIT Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–265（265 aa）	Mutation：K182G, L190G, Del(182-189)	RBF RIBOFLAVIN × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.53 Å
7LIT Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G Deposited 2021-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–265（265 aa）	Mutation：K182G, L190G, Del(182-189)	RBF RIBOFLAVIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, wait time 30 seconds	Resolution 2.53 Å
7MU1 Thermotoga maritima encapsulin shell Deposited 2021-05-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–264（264 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM Tris-HCl, pH 7.4, 150 mM NaCl and 5 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；blot force	Resolution 3.30 Å
7MU1 Thermotoga maritima encapsulin shell Deposited 2021-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–264（264 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM Tris-HCl, pH 7.4, 150 mM NaCl and 5 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；blot force	Resolution 3.30 Å
7MU1 Thermotoga maritima encapsulin shell Deposited 2021-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–264（264 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM Tris-HCl, pH 7.4, 150 mM NaCl and 5 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；blot force	Resolution 3.30 Å
7MU1 Thermotoga maritima encapsulin shell Deposited 2021-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–264（264 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM Tris-HCl, pH 7.4, 150 mM NaCl and 5 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；blot force	Resolution 3.30 Å
7MU1 Thermotoga maritima encapsulin shell Deposited 2021-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–264（264 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM Tris-HCl, pH 7.4, 150 mM NaCl and 5 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；blot force	Resolution 3.30 Å

12 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ENCAP_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–265； UniProt 1–265 Author chain AA； PDBConstruct 1–265； UniProt 1–265 Author chain AB； PDBConstruct 1–265； UniProt 1–265 Author chain B； PDBConstruct 1–265； UniProt 1–265 Author chain BA； PDBConstruct 1–265； UniProt 1–265 Author chain BB； PDBConstruct 1–265； UniProt 1–265 Author chain C； PDBConstruct 1–265； UniProt 1–265 Author chain CA； PDBConstruct 1–265； UniProt 1–265 Author chain CB； PDBConstruct 1–265； UniProt 1–265 Author chain D； PDBConstruct 1–265； UniProt 1–265 Author chain DA； PDBConstruct 1–265； UniProt 1–265 Author chain DB； PDBConstruct 1–265； UniProt 1–265 Author chain E； PDBConstruct 1–265； UniProt 1–265 Author chain EA； PDBConstruct 1–265； UniProt 1–265 Author chain EB； PDBConstruct 1–265； UniProt 1–265 Author chain F； PDBConstruct 1–265； UniProt 1–265 Author chain FA； PDBConstruct 1–265； UniProt 1–265 Author chain FB； PDBConstruct 1–265； UniProt 1–265 Author chain G； PDBConstruct 1–265； UniProt 1–265 Author chain GA； PDBConstruct 1–265； UniProt 1–265 Author chain GB； PDBConstruct 1–265； UniProt 1–265 Author chain H； PDBConstruct 1–265； UniProt 1–265 Author chain HA； PDBConstruct 1–265； UniProt 1–265 Author chain HB； PDBConstruct 1–265； UniProt 1–265 Author chain I； PDBConstruct 1–265； UniProt 1–265 Author chain IA； PDBConstruct 1–265； UniProt 1–265 Author chain J； PDBConstruct 1–265； UniProt 1–265 Author chain JA； PDBConstruct 1–265； UniProt 1–265 Author chain K； PDBConstruct 1–265； UniProt 1–265 Author chain KA； PDBConstruct 1–265； UniProt 1–265 Author chain L； PDBConstruct 1–265； UniProt 1–265 Author chain LA； PDBConstruct 1–265； UniProt 1–265 Author chain M； PDBConstruct 1–265； UniProt 1–265 Author chain MA； PDBConstruct 1–265； UniProt 1–265 Author chain N； PDBConstruct 1–265； UniProt 1–265 Author chain NA； PDBConstruct 1–265； UniProt 1–265 Author chain O； PDBConstruct 1–265； UniProt 1–265 Author chain OA； PDBConstruct 1–265； UniProt 1–265 Author chain P； PDBConstruct 1–265； UniProt 1–265 Author chain PA； PDBConstruct 1–265； UniProt 1–265 Author chain Q； PDBConstruct 1–265； UniProt 1–265 Author chain QA； PDBConstruct 1–265； UniProt 1–265 Author chain R； PDBConstruct 1–265； UniProt 1–265 Author chain RA； PDBConstruct 1–265； UniProt 1–265 Author chain S； PDBConstruct 1–265； UniProt 1–265 Author chain SA； PDBConstruct 1–265； UniProt 1–265 Author chain T； PDBConstruct 1–265； UniProt 1–265 Author chain TA； PDBConstruct 1–265； UniProt 1–265 Author chain U； PDBConstruct 1–265； UniProt 1–265 Author chain UA； PDBConstruct 1–265； UniProt 1–265 Author chain V； PDBConstruct 1–265； UniProt 1–265 Author chain VA； PDBConstruct 1–265； UniProt 1–265 Author chain W； PDBConstruct 1–265； UniProt 1–265 Author chain WA； PDBConstruct 1–265； UniProt 1–265 Author chain X； PDBConstruct 1–265； UniProt 1–265 Author chain XA； PDBConstruct 1–265； UniProt 1–265 Author chain Y； PDBConstruct 1–265； UniProt 1–265 Author chain YA； PDBConstruct 1–265； UniProt 1–265 Author chain Z； PDBConstruct 1–265； UniProt 1–265 Author chain ZA； PDBConstruct 1–265； UniProt 1–265

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9y8p
Deposition date deposition_date	2025-09-11
Structure title title	Cryo-EM structure of Thermotoga maritima encapsulin shell
Keywords keywords	ENCAPSULIN SHELL, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	— Å
Radius of gyration Rg (electron density) rg_electron	105.50 Å
Forward intensity I(0) i0	42521000000.00
Molecular weight molecular_weight	1827900.0 kDa
Excluded volume excluded_volume	2313700 Å³
Envelope volume envelope_volume	6210100 Å³
Hydration-shell volume shell_volume	501530 Å³
Envelope diameter envelope_diameter	248.9 Å
Shell Rg shell_rg	116.50 Å
Envelope Rg envelope_rg	88.89 Å
Shape Rg shape_rg	105.50 Å
Total Rg total_rg	105.70 Å
Total atoms total_atoms	129180
Residues n_residues	15900
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

▼

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

Maximum dimension Dmax dmax	249.0 Å
Rg (real space) rg_real	106.00 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	4.2560e+10
I(0) uncertainty (real space) i0_real_error	6.3590e+08
Rg (reciprocal space) rg_reciprocal	115.80 Å
I(0) (reciprocal space) i0_reciprocal	43910000000.0000
Solution quality estimate total_estimate	0.8600
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	182.6 Å
Skewness Skewness skewness	-0.481
Kurtosis Kurtosis kurtosis	-0.608
Angular range angular_range	— – 0.0750 Å⁻¹
Current regularization parameter α current_alpha	1.2500
Highest regularization parameter α highest_alpha	8184000000000000.0000
Real-space data points n_real_points	16
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 0.973; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

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	triclinic

Resolution resolution	3.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	46110

Description description	Type 1 encapsulin shell protein
Molecular weight formula_weight	30516.8 kDa
EC 编号 ec_number	3.4.-.-
Source method src_method	man
Copy count entity_count	60

Polymer type type	polypeptide(L)
Chain IDs strand_id	;U,A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB ;
Atom count atom_count	129180

Cryo-EM structure of Thermotoga maritima encapsulin shell

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

Type 1 encapsulin shell protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/y8/9y8p/9y8p.fit
pddf	/app/data/pr_computation/y8/9y8p/9y8p.pr.out
profile	/app/data/saxs_computation/y8/9y8p/9y8p.dat