SAXSdb — 4txq

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

Vacuolar protein sorting-associated protein VTA1 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 1–162	Fragment：UNP residues 1-162	Charged multivesicular body protein 1b × 1 （Q7LBR1）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；277.15 K；Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris	Resolution 2.21 Å R-free 0.227
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–162	Fragment：UNP residues 1-162	Charged multivesicular body protein 1b × 1 （Q7LBR1）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；277.15 K；Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris	Resolution 2.21 Å R-free 0.227

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 4TXQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LXL Lip5(mit)2 Deposited 2012-08-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–183（183 aa） Fragment：UNP residues 1-183	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 0.075；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] LIP5(1-183), 25 mM sodium phosphate, 50 mM sodium chloride, 0.5 mM DTT, 0.1 mM EDTA, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
2LXM Lip5-chmp5 Deposited 2012-08-29	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–168（168 aa） Fragment：UNP residues 1-168	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 75；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] LIP5(1-168), 0.5 mM [U-100% 13C; U-100% 15N] CHMP5(139-195), 25 mM sodium phosphate, 50 mM sodium chloride, 0.5 mM DTT, 0.1 mM EDTA, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
4TXP Crystal structure of LIP5 N-terminal domain Deposited 2014-07-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–162（162 aa） Fragment：UNP residues 1-162	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate	Resolution 3.01 Å R-free 0.286
4TXP Crystal structure of LIP5 N-terminal domain Deposited 2014-07-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–162（162 aa） Fragment：UNP residues 1-162	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate	Resolution 3.01 Å R-free 0.286
4TXP Crystal structure of LIP5 N-terminal domain Deposited 2014-07-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–162（162 aa） Fragment：UNP residues 1-162	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate	Resolution 3.01 Å R-free 0.286
4TXR Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM Deposited 2014-07-04	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 1–162（162 aa） Fragment：UNP residues 1-162	Not recorded	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；19% PEG 4000, 0.025 M sodium acetate	Resolution 1.00 Å R-free 0.180
4U7E The crystal structure of the complex of LIP5 NTD and IST1 MIM Deposited 2014-07-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–162（162 aa） Fragment：N-terminal domain (UNP residues 1-162)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；30% (w/v) PEG5000MME, 0.1 M ammonium sulfate , 0.1 M MES	Resolution 1.60 Å R-free 0.201

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VTA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–163； UniProt 1–162 Author chain B； PDBConstruct 2–163； UniProt 1–162

Charged multivesicular body protein 1b

Homo sapiens

UniProt Q7LBR1

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 C； UniProt 176–199	Fragment：UNP residues 176-199	Vacuolar protein sorting-associated protein VTA1 homolog × 1 （Q9NP79）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；277.15 K；Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris	Resolution 2.21 Å R-free 0.227
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 176–199	Fragment：UNP residues 176-199	Vacuolar protein sorting-associated protein VTA1 homolog × 1 （Q9NP79）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；277.15 K；Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris	Resolution 2.21 Å R-free 0.227

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 4TXQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JC1 Electron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer Deposited 2015-11-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 68 PDB declaration: 68-meric	Chain Ab 4–163（160 aa） Fragment：UNP residues 4-163 Chain Ad 4–163（160 aa） Fragment：UNP residues 4-163 Chain Af 4–163（160 aa） Fragment：UNP residues 4-163 Chain Ah 4–163（160 aa） Fragment：UNP residues 4-163 Chain Aj 4–163（160 aa） Fragment：UNP residues 4-163 Chain Al 4–163（160 aa） Fragment：UNP residues 4-163 Chain An 4–163（160 aa） Fragment：UNP residues 4-163 Chain Ap 4–163（160 aa） Fragment：UNP residues 4-163 Chain Ar 4–163（160 aa） Fragment：UNP residues 4-163 Chain At 4–163（160 aa） Fragment：UNP residues 4-163 Chain Av 4–163（160 aa） Fragment：UNP residues 4-163 Chain Ax 4–163（160 aa） Fragment：UNP residues 4-163 Chain Az 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bb 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bd 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bf 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bh 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bj 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bl 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bn 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bp 4–163（160 aa） Fragment：UNP residues 4-163 Chain Br 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bt 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bv 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bx 4–163（160 aa） Fragment：UNP residues 4-163 Chain Bz 4–163（160 aa） Fragment：UNP residues 4-163 Chain Cb 4–163（160 aa） Fragment：UNP residues 4-163 Chain Cd 4–163（160 aa） Fragment：UNP residues 4-163 Chain Cf 4–163（160 aa） Fragment：UNP residues 4-163 Chain Ch 4–163（160 aa） Fragment：UNP residues 4-163 Chain Cj 4–163（160 aa） Fragment：UNP residues 4-163 Chain Cl 4–163（160 aa） Fragment：UNP residues 4-163 Chain Cn 4–163（160 aa） Fragment：UNP residues 4-163 Chain Cp 4–163（160 aa） Fragment：UNP residues 4-163	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25 mM Tris, pH 8.0, 25 mM sodium chloride；pH 8；25 mM Tris, pH 8.0, 25 mM sodium chloride cryo-EM vitrification conditions Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset)；Cryogen ETHANE；Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset), and plunged into liquid ethane (VITROBOT MARK III).	Resolution 4.00 Å
4TXR Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM Deposited 2014-07-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 176–199（24 aa） Fragment：UNP residues 176-199	Not recorded	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；19% PEG 4000, 0.025 M sodium acetate	Resolution 1.00 Å R-free 0.180
6E8G CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ssDNA at 2.9 Angstrom resolution Deposited 2018-07-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain AA 1–199（199 aa） Chain AB 1–199（199 aa） Chain B 1–199（199 aa） Chain CA 1–199（199 aa） Chain CB 1–199（199 aa） Chain D 1–199（199 aa） Chain EA 1–199（199 aa） Chain EB 1–199（199 aa） Chain F 1–199（199 aa） Chain GA 1–199（199 aa） Chain GB 1–199（199 aa） Chain H 1–199（199 aa） Chain IA 1–199（199 aa） Chain IB 1–199（199 aa） Chain J 1–199（199 aa） Chain KA 1–199（199 aa） Chain KB 1–199（199 aa） Chain L 1–199（199 aa） Chain MA 1–199（199 aa） Chain MB 1–199（199 aa） Chain N 1–199（199 aa） Chain OA 1–199（199 aa） Chain OB 1–199（199 aa） Chain P 1–199（199 aa） Chain QA 1–199（199 aa） Chain QB 1–199（199 aa） Chain R 1–199（199 aa） Chain SA 1–199（199 aa） Chain SB 1–199（199 aa） Chain T 1–199（199 aa） Chain UA 1–199（199 aa） Chain UB 1–199（199 aa） Chain W 1–199（199 aa） Chain WA 1–199（199 aa） Chain Y 1–199（199 aa） Chain YA 1–199（199 aa）	Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；0 mm offset with 10 sec wait time and 2-4 sec blot	Resolution 2.90 Å
6TZ4 CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B+IST1 (right-handed) Deposited 2019-08-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain 02 1–199（199 aa） Chain A 1–199（199 aa） Chain BA 1–199（199 aa） Chain BB 1–199（199 aa） Chain C 1–199（199 aa） Chain DA 1–199（199 aa） Chain DB 1–199（199 aa） Chain E 1–199（199 aa） Chain FA 1–199（199 aa） Chain FB 1–199（199 aa） Chain G 1–199（199 aa） Chain HA 1–199（199 aa） Chain HB 1–199（199 aa） Chain I 1–199（199 aa） Chain JA 1–199（199 aa） Chain JB 1–199（199 aa） Chain K 1–199（199 aa） Chain LA 1–199（199 aa） Chain LB 1–199（199 aa） Chain M 1–199（199 aa） Chain NA 1–199（199 aa） Chain NB 1–199（199 aa） Chain O 1–199（199 aa） Chain PA 1–199（199 aa） Chain PB 1–199（199 aa） Chain Q 1–199（199 aa） Chain RA 1–199（199 aa） Chain RB 1–199（199 aa） Chain S 1–199（199 aa） Chain TA 1–199（199 aa） Chain V 1–199（199 aa） Chain VA 1–199（199 aa） Chain X 1–199（199 aa） Chain XA 1–199（199 aa） Chain Z 1–199（199 aa） Chain ZA 1–199（199 aa）	Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted with Whatman No. 1 filter paper for 4-8 seconds with a 0 mm offset at 19C and 100 percent humidity before plunging into liquid ethane	Resolution 3.20 Å
6TZ5 CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B+IST1 (left-handed) Deposited 2019-08-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 68 PDB declaration: 68-meric	Chain AA 1–199（199 aa） Chain AB 1–199（199 aa） Chain B 1–199（199 aa） Chain CA 1–199（199 aa） Chain CB 1–199（199 aa） Chain D 1–199（199 aa） Chain EA 1–199（199 aa） Chain EB 1–199（199 aa） Chain F 1–199（199 aa） Chain GA 1–199（199 aa） Chain GB 1–199（199 aa） Chain H 1–199（199 aa） Chain IA 1–199（199 aa） Chain IB 1–199（199 aa） Chain J 1–199（199 aa） Chain KA 1–199（199 aa） Chain KB 1–199（199 aa） Chain L 1–199（199 aa） Chain MA 1–199（199 aa） Chain MB 1–199（199 aa） Chain N 1–199（199 aa） Chain OA 1–199（199 aa） Chain OB 1–199（199 aa） Chain P 1–199（199 aa） Chain QA 1–199（199 aa） Chain QB 1–199（199 aa） Chain R 1–199（199 aa） Chain SA 1–199（199 aa） Chain T 1–199（199 aa） Chain UA 1–199（199 aa） Chain W 1–199（199 aa） Chain WA 1–199（199 aa） Chain Y 1–199（199 aa） Chain YA 1–199（199 aa）	Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted with Whatman No. 1 filter paper for 4-8 seconds with a 0 mm offset at 19C and 100 percent humidity before plunging into liquid ethane	Resolution 3.10 Å
6TZ9 CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B only Deposited 2019-08-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 26 PDB declaration: 26-meric	Chain A 1–199（199 aa） Chain AA 1–199（199 aa） Chain B 1–199（199 aa） Chain C 1–199（199 aa） Chain D 1–199（199 aa） Chain E 1–199（199 aa） Chain F 1–199（199 aa） Chain G 1–199（199 aa） Chain H 1–199（199 aa） Chain I 1–199（199 aa） Chain J 1–199（199 aa） Chain K 1–199（199 aa） Chain L 1–199（199 aa） Chain M 1–199（199 aa） Chain N 1–199（199 aa） Chain O 1–199（199 aa） Chain P 1–199（199 aa） Chain Q 1–199（199 aa） Chain R 1–199（199 aa） Chain S 1–199（199 aa） Chain T 1–199（199 aa） Chain V 1–199（199 aa） Chain W 1–199（199 aa） Chain X 1–199（199 aa） Chain Y 1–199（199 aa） Chain Z 1–199（199 aa）	Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E Mutation：K37E	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted with Whatman No. 1 filter paper for 4-8 seconds with a 0 mm offset at 19C and 100 percent humidity before plunging into liquid ethane	Resolution 6.20 Å
8V2Q CHMP1B/IST1 ssRNA bound copolymer Deposited 2023-11-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 182 PDB declaration: 182-meric	Chain A 1–199（199 aa）	Mutation：M136V	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8V2R CryoEM of ssDNA bound CHMP1B/IST1 copolymer assembly Deposited 2023-11-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric	Chain A 1–199（199 aa）	Mutation：M136V	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8V2S CHMP1B/IST1 dsDNA bound copolymer Deposited 2023-11-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric	Chain A 1–199（199 aa）	Mutation：M136V	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.72 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHM1B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–25； UniProt 176–199 Author chain D； PDBConstruct 2–25； UniProt 176–199

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	4txq
Deposition date deposition_date	2014-07-04
Structure title title	Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM
Keywords keywords	MIT, MIT domain, Protein Transport, ESCRT; PROTEIN TRANSPORT
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	27.14 Å
Radius of gyration Rg (electron density) rg_electron	26.80 Å
Forward intensity I(0) i0	27066500.00
Molecular weight molecular_weight	40003.0 kDa
Excluded volume excluded_volume	50110 Å³
Envelope volume envelope_volume	63685 Å³
Hydration-shell volume shell_volume	21514 Å³
Envelope diameter envelope_diameter	89.3 Å
Shell Rg shell_rg	31.82 Å
Envelope Rg envelope_rg	26.73 Å
Shape Rg shape_rg	26.75 Å
Total Rg total_rg	27.53 Å
Total atoms total_atoms	2810
Residues n_residues	354
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	91.6 Å
Rg (real space) rg_real	27.43 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	2.7070e+07
I(0) uncertainty (real space) i0_real_error	4.4330e+05
Rg (reciprocal space) rg_reciprocal	27.34 Å
I(0) (reciprocal space) i0_reciprocal	27060000.0000
Solution quality estimate total_estimate	0.8317
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.500
Kurtosis Kurtosis kurtosis	-0.518
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5279000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.732; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.692; Smooth: 0.920

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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	Vacuolar protein sorting-associated protein VTA1 homolog
Molecular weight formula_weight	18792.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3008

SMAALAPLPPLPAQFKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEALKKQLGDNEAITQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFYTASLLIDVITVFGELTDENVKHRKYARWKATYIHNCLKNGETP

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	Charged multivesicular body protein 1b
Molecular weight formula_weight	2719.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SVGTSVASAEQDELSQRLARLRDQV

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	198

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4txqA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	270 — Vacuolar protein sorting-associated protein vta1

Domain ID domain_id	4txqB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	270 — Vacuolar protein sorting-associated protein vta1

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8. Citations (1)

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Unit-cell length a length_a	52.936 Å
Unit-cell length b length_b	55.536 Å
Unit-cell length c length_c	195.359 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	8

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

Resolution resolution	2.210 Å
Low-resolution limit resolution_low	41.076 Å
R factor r_factor	0.1955
R_work r_work	0.1932
R_free r_free	0.2266

fit	/app/data/saxs_computation/tx/4txq/4txq.fit
pddf	/app/data/pr_computation/tx/4txq/4txq.pr.out
profile	/app/data/saxs_computation/tx/4txq/4txq.dat

Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM

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

Vacuolar protein sorting-associated protein VTA1 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Charged multivesicular body protein 1b

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 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)