9xou

CryoEM structure of LacY with Trimbody

Method: ELECTRON MICROSCOPY D_max: 156.4 Å Quality: GOOD

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

H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

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 × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 2–205 Chain B； UniProt 2–205 Chain C； UniProt 2–205	Not recorded	LacY-nanobody-TAIL × 3 Lactose permease × 3 （P02920）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.50 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 9XOU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1VLW Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution Deposited 2004-08-18	Different construct Different mutation/modification 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 1–205（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION,SITTING DROP,NANODROP；pH 7.5；277 K；22.5% PEG-1000, 0.1M Tris pH 7.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K	Resolution 2.30 Å R-free 0.221
1VLW Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution Deposited 2004-08-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–205（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION,SITTING DROP,NANODROP；pH 7.5；277 K；22.5% PEG-1000, 0.1M Tris pH 7.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K	Resolution 2.30 Å R-free 0.221
1VLW Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution Deposited 2004-08-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–205（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION,SITTING DROP,NANODROP；pH 7.5；277 K；22.5% PEG-1000, 0.1M Tris pH 7.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K	Resolution 2.30 Å R-free 0.221
1VLW Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution Deposited 2004-08-18	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa） Chain C 1–205（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION,SITTING DROP,NANODROP；pH 7.5；277 K；22.5% PEG-1000, 0.1M Tris pH 7.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K	Resolution 2.30 Å R-free 0.221
1WA3 Mechanism of the Class I KDPG aldolase Deposited 2004-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa） Chain C 1–205（205 aa）	Not recorded	PYR PYRUVIC ACID × 3 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.075M SODIUM ACETATE, 0.1M AMMONIUM SULPHATE, 28%W/V PEG4000, pH 4.60	Resolution 1.90 Å R-free 0.239
1WA3 Mechanism of the Class I KDPG aldolase Deposited 2004-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 1–205（205 aa） Chain E 1–205（205 aa） Chain F 1–205（205 aa）	Not recorded	PYR PYRUVIC ACID × 3 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.075M SODIUM ACETATE, 0.1M AMMONIUM SULPHATE, 28%W/V PEG4000, pH 4.60	Resolution 1.90 Å R-free 0.239
5KP9 Structure of Nanoparticle Released from Enveloped Protein Nanoparticle Deposited 2016-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain B 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Phosphate-buffered saline cryo-EM vitrification conditions Cryogen ETHANE；11 second blot, 0 mm offset	Resolution 5.70 Å
5KP9 Structure of Nanoparticle Released from Enveloped Protein Nanoparticle Deposited 2016-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Phosphate-buffered saline cryo-EM vitrification conditions Cryogen ETHANE；11 second blot, 0 mm offset	Resolution 5.70 Å
5KP9 Structure of Nanoparticle Released from Enveloped Protein Nanoparticle Deposited 2016-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 5 PDB declaration: pentameric	Chain B 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Phosphate-buffered saline cryo-EM vitrification conditions Cryogen ETHANE；11 second blot, 0 mm offset	Resolution 5.70 Å
5KP9 Structure of Nanoparticle Released from Enveloped Protein Nanoparticle Deposited 2016-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric	Chain B 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Phosphate-buffered saline cryo-EM vitrification conditions Cryogen ETHANE；11 second blot, 0 mm offset	Resolution 5.70 Å
5KP9 Structure of Nanoparticle Released from Enveloped Protein Nanoparticle Deposited 2016-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Phosphate-buffered saline cryo-EM vitrification conditions Cryogen ETHANE；11 second blot, 0 mm offset	Resolution 5.70 Å
7B3Y Structure of a nanoparticle for a COVID-19 vaccine candidate Deposited 2020-12-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain B 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8A8N Structure of self-assembling engineered protein nanocage (EPN) fused with hepatitis A pX protein Deposited 2022-06-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7；PBS cryo-EM vitrification conditions Cryogen ETHANE；Blot time 4-5 s.	Resolution 6.70 Å
8E01 Structure of engineered nano-cage fusion protein Deposited 2022-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.1；Tris, 100 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8E01 Structure of engineered nano-cage fusion protein Deposited 2022-08-08	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 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.1；Tris, 100 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8E01 Structure of engineered nano-cage fusion protein Deposited 2022-08-08	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 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.1；Tris, 100 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8E01 Structure of engineered nano-cage fusion protein Deposited 2022-08-08	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 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.1；Tris, 100 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8E01 Structure of engineered nano-cage fusion protein Deposited 2022-08-08	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 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.1；Tris, 100 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8JGA Cryo-EM structure of Mi3 fused with FKBP Deposited 2023-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å
8JGC Cryo-EM structure of Mi3 fused with LOV2 Deposited 2023-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å
8SZZ CryoEM Structure of Computationally Designed Nanocage O32-ZL4 Deposited 2023-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain I 1–205（205 aa） Chain J 1–205（205 aa） Chain K 1–205（205 aa） Chain L 1–205（205 aa） Chain M 1–205（205 aa） Chain N 1–205（205 aa） Chain O 1–205（205 aa） Chain U 1–205（205 aa） Chain Y 1–205（205 aa） Chain Z 1–205（205 aa） Chain a 1–205（205 aa） Chain b 1–205（205 aa） Chain c 1–205（205 aa） Chain d 1–205（205 aa） Chain e 1–205（205 aa） Chain f 1–205（205 aa） Chain g 1–205（205 aa） Chain h 1–205（205 aa） Chain i 1–205（205 aa） Chain j 1–205（205 aa） Chain k 1–205（205 aa） Chain l 1–205（205 aa） Chain m 1–205（205 aa） Chain n 1–205（205 aa）	Not recorded	NA SODIUM ION × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM Tris/HCl pH 7.5, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8TVB Ghanaian virus fusion glycoprotein (GhV F) Deposited 2023-08-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–205（204 aa） Chain B 2–205（204 aa） Chain C 2–205（204 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8TYC Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1 Deposited 2023-08-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain a 2–205（204 aa） Chain b 2–205（204 aa） Chain c 2–205（204 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8TYE Lassa GPC (strain Josiah) bound to rabbit polyclonal fusion-peptide-targeting antibody FP-1 Deposited 2023-08-25	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain a 2–205（204 aa） Chain b 2–205（204 aa） Chain c 2–205（204 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9FO3 Structure of a gp140 SpyTag-SpyCatcher mi3 nanoparticle including mi3 density only. Deposited 2024-06-11	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain 0 1–205（205 aa） Chain 1 1–205（205 aa） Chain 2 1–205（205 aa） Chain 3 1–205（205 aa） Chain 4 1–205（205 aa） Chain 5 1–205（205 aa） Chain 6 1–205（205 aa） Chain 7 1–205（205 aa） Chain A 1–205（205 aa） Chain B 1–205（205 aa） Chain C 1–205（205 aa） Chain D 1–205（205 aa） Chain E 1–205（205 aa） Chain F 1–205（205 aa） Chain G 1–205（205 aa） Chain H 1–205（205 aa） Chain I 1–205（205 aa） Chain J 1–205（205 aa） Chain K 1–205（205 aa） Chain L 1–205（205 aa） Chain M 1–205（205 aa） Chain N 1–205（205 aa） Chain O 1–205（205 aa） Chain P 1–205（205 aa） Chain Q 1–205（205 aa） Chain R 1–205（205 aa） Chain S 1–205（205 aa） Chain T 1–205（205 aa） Chain U 1–205（205 aa） Chain V 1–205（205 aa） Chain W 1–205（205 aa） Chain X 1–205（205 aa） Chain Y 1–205（205 aa） Chain Z 1–205（205 aa） Chain a 1–205（205 aa） Chain b 1–205（205 aa） Chain c 1–205（205 aa） Chain d 1–205（205 aa） Chain e 1–205（205 aa） Chain f 1–205（205 aa） Chain g 1–205（205 aa） Chain h 1–205（205 aa） Chain i 1–205（205 aa） Chain j 1–205（205 aa） Chain k 1–205（205 aa） Chain l 1–205（205 aa） Chain m 1–205（205 aa） Chain n 1–205（205 aa） Chain o 1–205（205 aa） Chain p 1–205（205 aa） Chain q 1–205（205 aa） Chain r 1–205（205 aa） Chain s 1–205（205 aa） Chain t 1–205（205 aa） Chain u 1–205（205 aa） Chain v 1–205（205 aa） Chain w 1–205（205 aa） Chain x 1–205（205 aa） Chain y 1–205（205 aa） Chain z 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.30 Å
9UAQ CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody Deposited 2025-04-01	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 2–205（204 aa） Chain B 2–205（204 aa） Chain C 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.29 Å
9UBR CryoEM structure of human Galectin-10 with iTrimbody Deposited 2025-04-03	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 2–205（204 aa） Chain B 2–205（204 aa） Chain C 2–205（204 aa） Chain D 2–205（204 aa） Chain E 2–205（204 aa） Chain F 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å
9UCL CryoEM structure of IgV domain of human Nectin-4 with Trimbody Deposited 2025-04-04	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 2–205（204 aa） Chain B 2–205（204 aa） Chain C 2–205（204 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.43 Å

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

View Construct and Data Evidence

UniProt name	Q9WXS1_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 118–321； UniProt 2–205 Author chain B； PDBConstruct 118–321； UniProt 2–205 Author chain C； PDBConstruct 118–321； UniProt 2–205

Lactose permease

Escherichia coli K-12

UniProt P02920

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 × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain G； UniProt 1–417 Chain H； UniProt 1–417 Chain I； UniProt 1–417	Not recorded	H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase × 3 （Q9WXS1） LacY-nanobody-TAIL × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XOU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PV6 Crystal structure of lactose permease Deposited 2003-06-26	Different construct Different mutation/modification 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 1–417（417 aa）	Mutation：C154G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.337
1PV6 Crystal structure of lactose permease Deposited 2003-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–417（417 aa）	Mutation：C154G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.337
1PV7 Crystal structure of lactose permease with TDG Deposited 2003-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–417（417 aa）	Mutation：C154G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.296
1PV7 Crystal structure of lactose permease with TDG Deposited 2003-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–417（417 aa）	Mutation：C154G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.296
2CFP Sugar Free Lactose Permease at acidic pH Deposited 2006-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–417（417 aa）	Mutation：YES	HG MERCURY (II) ION × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.30 Å R-free 0.328
2CFQ Sugar Free Lactose Permease at neutral pH Deposited 2006-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–417（417 aa）	Mutation：YES	HG MERCURY (II) ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.95 Å R-free 0.298
2V8N Wild-type Structure of Lactose Permease Deposited 2007-08-09	Different construct Different mutation/modification 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 1–417（417 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.60 Å R-free 0.333
2V8N Wild-type Structure of Lactose Permease Deposited 2007-08-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–417（417 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.60 Å R-free 0.333
2Y5Y Crystal structure of LacY in complex with an affinity inactivator Deposited 2011-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–417（417 aa） Chain B 1–417（417 aa）	Mutation：YES Mutation：YES	BA BARIUM ION × 2 TGA 2-sulfanylethyl beta-D-galactopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 3.38 Å R-free 0.303
4ZYR Crystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG) Deposited 2015-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–417（417 aa）	Mutation：G46W, G262W	9PG 4-nitrophenyl alpha-D-galactopyranoside × 1 BNG nonyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；1.0 M NaCl 0.05 M Tris (pH8.0) 26% PEG 600	Resolution 3.31 Å R-free 0.278
4ZYR Crystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG) Deposited 2015-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–417（417 aa）	Mutation：G46W, G262W	9PG 4-nitrophenyl alpha-D-galactopyranoside × 1 BNG nonyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；1.0 M NaCl 0.05 M Tris (pH8.0) 26% PEG 600	Resolution 3.31 Å R-free 0.278
5GXB crystal structure of a LacY/Nanobody complex Deposited 2016-09-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–417（417 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM MES pH 6.0, 100mM (NH4)2C4H4O6, 43% PEG 400	Resolution 3.30 Å R-free 0.346
6C9W Crystal Structure of a ligand bound LacY/Nanobody Complex Deposited 2018-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–417（417 aa） Fragment：Full	Mutation：G46W, G262W	9PG 4-nitrophenyl alpha-D-galactopyranoside × 1 BNG nonyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；295 K；0.1 M MgCl2, 28% PEG1000, 0.1 M Tris-HCl, pH 8.5	Resolution 3.00 Å R-free 0.295
8Y9Y Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C) Deposited 2024-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 315–334（20 aa）	Mutation：T1M,R2A,L3K,A4K,G5T,C53A	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8YA0 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) Deposited 2024-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 316–332（17 aa）	Mutation：R2A, L3K, A4K, G5T, C14T, F17L	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
8YA2 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C) Deposited 2024-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 315–334（20 aa）	Mutation：T1M,R2A,L3K,A4K,G5T,E45C,C53A	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8YA3 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) treated with DTT Deposited 2024-02-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 315–334（20 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LACY_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–417； UniProt 1–417 Author chain H； PDBConstruct 1–417； UniProt 1–417 Author chain I； PDBConstruct 1–417； UniProt 1–417

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9xou
Deposition date deposition_date	2025-11-15
Structure title title	CryoEM structure of LacY with Trimbody
Keywords keywords	STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	57.21 Å
Radius of gyration Rg (electron density) rg_electron	58.14 Å
Forward intensity I(0) i0	1198320000.00
Molecular weight molecular_weight	316670.0 kDa
Excluded volume excluded_volume	406970 Å³
Envelope volume envelope_volume	599000 Å³
Hydration-shell volume shell_volume	88371 Å³
Envelope diameter envelope_diameter	167.9 Å
Shell Rg shell_rg	58.15 Å
Envelope Rg envelope_rg	56.03 Å
Shape Rg shape_rg	58.21 Å
Total Rg total_rg	57.84 Å
Total atoms total_atoms	22382
Residues n_residues	2870
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	156.4 Å
Rg (real space) rg_real	56.94 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	1.1980e+09
I(0) uncertainty (real space) i0_real_error	1.8210e+07
Rg (reciprocal space) rg_reciprocal	57.40 Å
I(0) (reciprocal space) i0_reciprocal	1199000000.0000
Solution quality estimate total_estimate	0.8461
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	92.7 Å
Skewness Skewness skewness	-0.039
Kurtosis Kurtosis kurtosis	-0.771
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	44750000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.999; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Molecular weight formula_weight	36127.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	22382

MKEIAKIVAELLRGIARIIDDIKGRDREEEVEILAKAVEKTGKPEDVRLALEAAERGVTLDQAKAIAQILSMPNLTDEQKRGFVQSLLDDPSVSKEILAEAKKLNEHQAAKAEEAARKMEELFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTVIKALSVLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGCTEAAALEHHHHHH

来源 Source

来源生物 organism	Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
NCBI Class编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	LacY-nanobody-TAIL
Molecular weight formula_weight	28210.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

MQVQLVESGGRLVQAGDSLRLSCAASGRTFTTYLMGWFRQAPGKEREFVAAIRWSGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKLEDTAVYYCAAAARPSYSGDYGYTEALRYDYWGQGTLVAVVKTVEDAFLALLALEQHLGVQPADLAALAEKLNLSQLLELGELLKAAGHPLAPQVEALLKEKLKAASAAEAAGVIFQALVKDEELGKKILEWAKEFGTEEAKKAIEIAEKAYELYKKYGSWSHPQFEK

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Lactose permease
Molecular weight formula_weight	49236.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFSFNAGAPAVEAFIEKVSRRSNFEFGRARMFGAVGWALVASIVGIMFTINNQFVFWLGSGMALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSSTYDVFDQQFANFFTSFFATGEQGTRVFWYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGSFKYITSQFEVRFSATIYLVAFAFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVAWSHPQFEKGSHHHHHHHHHH

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Resolution resolution	2.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	371100

fit	/app/data/saxs_computation/xo/9xou/9xou.fit
pddf	/app/data/pr_computation/xo/9xou/9xou.pr.out
profile	/app/data/saxs_computation/xo/9xou/9xou.dat

CryoEM structure of LacY with Trimbody

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

H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

State in the Current Structure

Other States of the Same Protein in the Database

Lactose permease

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

冷冻电镜 EM 3D

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)