SAXSdb — 9rpr

▼

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

LPS-assembly lipoprotein LptE

Shigella flexneri

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–193	Not recorded	LPS-assembly protein LptD × 1 （P31554） LPS-assembly lipoprotein LptM × 1 （P0ADN6） PLM PALMITIC ACID × 1 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.78 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 9RPR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Q35 Structure of a membrane protein Deposited 2014-04-11	Different construct 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 B 19–193（175 aa）	Not recorded	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 7 SO4 SULFATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；10 mM sodium citrate (pH 5.6), 300mM lithium sulfate, 8% PEG 400, 100mM glycine, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.39 Å R-free 0.231
9I92 Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 1) Deposited 2025-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–193（175 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 3 A1I1D 1-[4,7-bis(2-chloranylethanoyl)-1,4,7-triazonan-1-yl]-2-chloranyl-ethanone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.41 Å
9I93 Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 2) Deposited 2025-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–193（175 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 3 KZ0 2,4,6-tris(chloromethyl)-1,3,5-triazine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9I94 Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 3) Deposited 2025-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–193（175 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 7 KZ0 2,4,6-tris(chloromethyl)-1,3,5-triazine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.84 Å
9I95 Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 4) Deposited 2025-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–193（175 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 2 A1I1E 1-[7,10-bis(2-chloranylethanoyl)-3,7,10-triazatricyclo[3.3.3.0^{1,5}]undecan-3-yl]-2-chloranyl-ethanone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.35 Å
9I96 Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 5) Deposited 2025-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–193（175 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 3 R06 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å
9I97 Cryo-EM structure of Shigella flexneri LptDE in complex with a Bicyclic Peptide binder (Compound 12) Deposited 2025-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–193（175 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 1 A1I1D 1-[4,7-bis(2-chloranylethanoyl)-1,4,7-triazonan-1-yl]-2-chloranyl-ethanone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.48 Å
9I98 Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 13) Deposited 2025-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–193（175 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 3 R06 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9Q8N Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 16) Deposited 2025-02-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–169（151 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 2 PLM PALMITIC ACID × 1 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 1 A1I4O 1,3,5-tris(2-chloroethylsulfonyl)-1,3,5-triazinane × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
9RPS Cryo-EM structure of Shigella flexneri LptDE in complex with RTP45 superinfection exclusion protein from RTP bacteriophage and endogenous LptM Deposited 2025-06-25	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–193（193 aa）	Not recorded	PLM PALMITIC ACID × 1 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9RPT Cryo-EM structure of the open state of Shigella flexneri LptDE bound by the RBP of Oekolampad phage Deposited 2025-06-25	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–193（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9RPW Cryo-EM structure of Shigella flexneri LptDE dimer: closed-state unbound and open-state bound by Oekolampad phage RBP Deposited 2025-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–193（193 aa） Chain E 1–193（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9RQI Cryo-EM structure of Shigella flexneri LptDE bound by phage RBP reveals N-terminal strand insertion into lateral gate Deposited 2025-06-25	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–193（193 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å

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

View Construct and Data Evidence

UniProt name	LPTE_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–193； UniProt 1–193

LPS-assembly protein LptD

OrganismNot specified

UniProt P31554

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–784	Not recorded	LPS-assembly lipoprotein LptE × 1 （Q83LX4） LPS-assembly lipoprotein LptM × 1 （P0ADN6） PLM PALMITIC ACID × 1 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.78 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 9RPR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4RHB Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane Deposited 2014-10-01	Different construct 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 203–784（582 aa）	Not recorded	CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.35 Å R-free 0.338
4RHB Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane Deposited 2014-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 203–784（582 aa）	Not recorded	CL CHLORIDE ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.35 Å R-free 0.338
9FZ5 Cryo-EM structure of LptDE-YedD complex from Escherichia Coli Deposited 2024-07-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–784（759 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Blot 3-4 seconds	Resolution 3.57 Å
9I9Z LpDE from Escherichia coli Deposited 2025-02-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.74 Å
9IA0 LpDE from Escherichia coli Deposited 2025-02-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å
9IA2 LpDEM from Escherichia coli Deposited 2025-02-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.47 Å
9IA5 LpDEM from Escherichia coli Deposited 2025-02-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
9KN3 Cryo-EM structure of LptDEM complex from Escherichia coli Deposited 2024-11-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–784（760 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
9P1U beta-barrel assembly machine from Escherichia coli in an late state of LptD assembly Deposited 2025-06-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–784（784 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9Y0P Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode I Deposited 2025-08-28	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 B 26–37（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 NO3 NITRATE ION × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium acetate hydrate, 20% w/v Polyethylene glycol 3,350	Resolution 1.47 Å R-free 0.210
9Y0P Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode I Deposited 2025-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 26–37（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 NO3 NITRATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium acetate hydrate, 20% w/v Polyethylene glycol 3,350	Resolution 1.47 Å R-free 0.210
9Y0Q Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode II Deposited 2025-08-28	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 B 26–37（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium nitrate hexahydrate, 20% w/v Polyethylene glycol 3,350	Resolution 1.47 Å R-free 0.213

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

View Construct and Data Evidence

UniProt name	LPTD_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–784； UniProt 1–784

LPS-assembly lipoprotein LptM

OrganismNot specified

UniProt P0ADN6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 20–67	Not recorded	LPS-assembly lipoprotein LptE × 1 （Q83LX4） LPS-assembly protein LptD × 1 （P31554） PLM PALMITIC ACID × 1 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.78 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 9RPR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H1R Crystal structure of LptDE-YifL complex Deposited 2022-10-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–67（67 aa）	Not recorded	PCJ (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；175 mM citric acid/Bis-Tris (pH 5.0), 17% (v/v) PEG3350 and 3% methanol (as additive)	Resolution 2.98 Å R-free 0.264
8H1R Crystal structure of LptDE-YifL complex Deposited 2022-10-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–67（67 aa）	Not recorded	PCJ (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；175 mM citric acid/Bis-Tris (pH 5.0), 17% (v/v) PEG3350 and 3% methanol (as additive)	Resolution 2.98 Å R-free 0.264
9IA2 LpDEM from Escherichia coli Deposited 2025-02-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–67（67 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.47 Å
9IA5 LpDEM from Escherichia coli Deposited 2025-02-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–67（67 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
9KN3 Cryo-EM structure of LptDEM complex from Escherichia coli Deposited 2024-11-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 20–67（48 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
9RPS Cryo-EM structure of Shigella flexneri LptDE in complex with RTP45 superinfection exclusion protein from RTP bacteriophage and endogenous LptM Deposited 2025-06-25	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 20–67（48 aa）	Not recorded	PLM PALMITIC ACID × 1 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LPTM_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–48； UniProt 20–67

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9rpr
Deposition date deposition_date	2025-06-25
最后修订 last_revision	2025-12-10
Structure title title	Cryo-EM structure of LptDEM complex containing Shigella flexneri LptE and endogenous E. coli LptD and LptM
Keywords keywords	lipopolysaccharide transport, outer membrane protein complex, beta-barrel, lipoprotein, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	33.29 Å
Radius of gyration Rg (electron density) rg_electron	33.06 Å
Forward intensity I(0) i0	180051000.00
Molecular weight molecular_weight	104930.0 kDa
Excluded volume excluded_volume	130150 Å³
Envelope volume envelope_volume	171140 Å³
Hydration-shell volume shell_volume	44091 Å³
Envelope diameter envelope_diameter	119.3 Å
Shell Rg shell_rg	39.30 Å
Envelope Rg envelope_rg	32.97 Å
Shape Rg shape_rg	33.06 Å
Total Rg total_rg	33.55 Å
Total atoms total_atoms	7403
Residues n_residues	912
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	112.1 Å
Rg (real space) rg_real	33.44 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	1.8010e+08
I(0) uncertainty (real space) i0_real_error	2.8500e+06
Rg (reciprocal space) rg_reciprocal	33.38 Å
I(0) (reciprocal space) i0_reciprocal	180000000.0000
Solution quality estimate total_estimate	0.8504
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.4 Å
Skewness Skewness skewness	0.510
Kurtosis Kurtosis kurtosis	-0.061
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25820000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.638

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	LPS-assembly lipoprotein LptE
Molecular weight formula_weight	22240.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	7403

MRYLATLLLSLAVLITAGCGWHLRDTTQVPSTMKVMILDSGDPNGPLSRAVRNQLRLNGVELLDKETTRKDVPSLRLGKVSIAKDTASVFRNGQTAEYQMIMTVNATVLIPGRDIYPISAKVFRSFFDNPQMALAKDNEQDMIVKEMYDRAAEQLIRKLPSIRAADIRSDEEQTSTTTDTPATPARVSTMLGNHHHHHH

来源 Source

来源生物 organism	Shigella flexneri
NCBI Class编号 ncbi_taxonomy_id	623
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	LPS-assembly protein LptD
Molecular weight formula_weight	89754.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MKKRIPTLLATMIATALYSQQGLAADLASQCMLGVPSYDRPLVQGDTNDLPVTINADHAKGDYPDDAVFTGSVDIMQGNSRLQADEVQLHQKEAPGQPEPVRTVDALGNVHYDDNQVILKGPKGWANLNTKDTNVWEGDYQMVGRQGRGKADLMKQRGENRYTILDNGSFTSCLPGSDTWSVVGSEIIHDREEQVAEIWNARFKVGPVPIFYSPYLQLPVGDKRRSGFLIPNAKYTTTNYFEFYLPYYWNIAPNMDATITPHYMHRRGNIMWENEFRYLSQAGAGLMELDYLPSDKVYEDEHPNDDSSRRWLFYWNHSGVMDQVWRFNVDYTKVSDPSYFNDFDNKYGSSTDGYATQKFSVGYAVQNFNATVSTKQFQVFSEQNTSSYSAEPQLDVNYYQNDVGPFDTRIYGQAVHFVNTRDDMPEATRVHLEPTINLPLSNNWGSINTEAKLLATHYQQTNLDWYNSRNTTKLDESVNRVMPQFKVDGKMVFERDMEMLAPGYTQTLEPRAQYLYVPYRDQSDIYNYDSSLLQSDYSGLFRDRTYGGLDRIASANQVTTGVTSRIYDDAAVERFNISVGQIYYFTESRTGDDNITWENDDKTGSLVWAGDTYWRISERWGLRGGIQYDTRLDNVATSNSSIEYRRDEDRLVQLNYRYASPEYIQATLPKYYSTAEQYKNGISQVGAVASWPIADRWSIVGAYYYDTNANKQADSMLGVQYSSCCYAIRVGYERKLNGWDNDKQHAVYDNAIGFNIELRGLSSNYGLGTQEMLRSNILPYQNTL

Entity 3 Entity 3 polymer

Description description	LPS-assembly lipoprotein LptM
Molecular weight formula_weight	5103.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

CGLKGPLYFPPADKNAPPPTKPVETQTQSTVPDKNDRATGDGPSQVNY

Entity 4 Entity 4 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(2S)-propane-1,2-diyl dihexadecanoate
Molecular weight formula_weight	552.9 kDa
Source method src_method	syn
Copy count entity_count	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	—

Resolution resolution	2.78 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	112032

fit	/app/data/saxs_computation/rp/9rpr/9rpr.fit
pddf	/app/data/pr_computation/rp/9rpr/9rpr.pr.out
profile	/app/data/saxs_computation/rp/9rpr/9rpr.dat

Cryo-EM structure of LptDEM complex containing Shigella flexneri LptE and endogenous E. coli LptD and LptM

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

LPS-assembly lipoprotein LptE

State in the Current Structure

Other States of the Same Protein in the Database

LPS-assembly protein LptD

State in the Current Structure

Other States of the Same Protein in the Database

LPS-assembly lipoprotein LptM

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)