SAXSdb — 4utq

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

MEMBRANE PROTEIN INSERTASE YIDC

OrganismNot specified

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 1–548	Not recorded	ATP SYNTHASE SUBUNIT C × 1 （P68699）	ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,	Resolution 8.00 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 4UTQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10	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 26–340（315 aa） Fragment：UNP residues 26-340	Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.249
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10	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 26–340（315 aa） Fragment：UNP residues 26-340	Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.249
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 26–340（315 aa） Fragment：UNP residues 26-340 Chain B 26–340（315 aa） Fragment：UNP residues 26-340	Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.249
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22	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 56–329（274 aa） Fragment：UNP residues 56-329	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 5 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K	Resolution 1.80 Å R-free 0.213
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22	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 56–329（274 aa） Fragment：UNP residues 56-329	Non-standard monomer：Yes (specific site not provided by mmCIF)	PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 4 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K	Resolution 1.80 Å R-free 0.213
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 56–329（274 aa） Fragment：UNP residues 56-329 Chain B 56–329（274 aa） Fragment：UNP residues 56-329	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 10 PG4 TETRAETHYLENE GLYCOL × 2 PGE TRIETHYLENE GLYCOL × 6 EDO 1,2-ETHANEDIOL × 14 2PE NONAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K	Resolution 1.80 Å R-free 0.213
5MG3 EM fitted model of bacterial holo-translocon Deposited 2016-11-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 2–548（547 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.00 Å
9RBF Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the membrane protein insertase SecYEG-YidC Deposited 2025-05-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 61-meric	Chain 9 1–548（548 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.44 Å

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YIDC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–548； UniProt 1–548

ATP SYNTHASE SUBUNIT C

OrganismNot specified

UniProt P68699

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 Z； UniProt 1–79	Fragment：MEMBRANE DOMAIN	MEMBRANE PROTEIN INSERTASE YIDC × 1 （P25714）	ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,	Resolution 8.00 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 4UTQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A91 SUBUNIT C OF THE F1FO ATP SYNTHASE OF ESCHERICHIA COLI; NMR, 10 STRUCTURES Deposited 1998-04-15	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 1–79（79 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；300 K	Resolution not provided
1ATY DETERMINATION OF LOCAL PROTEIN STRUCTURE BY SPIN LABEL DIFFERENCE 2D NMR: THE REGION NEIGHBORING ASP61 OF SUBUNIT C OF THE F1FO ATP SYNTHASE Deposited 1994-10-05	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 1–79（79 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1C0V SUBUNIT C OF THE F1FO ATP SYNTHASE OF ESCHERICHIA COLI; NMR, 10 STRUCTURES Deposited 1999-07-22	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 1–79（79 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；300 K；Pressure 1 NMR sample composition 4:4:1	Resolution not provided
1C17 A1C12 SUBCOMPLEX OF F1FO ATP SYNTHASE Deposited 1999-07-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 1–79（79 aa） Chain B 1–79（79 aa） Chain C 1–79（79 aa） Chain D 1–79（79 aa） Chain E 1–79（79 aa） Chain F 1–79（79 aa） Chain G 1–79（79 aa） Chain H 1–79（79 aa） Chain I 1–79（79 aa） Chain J 1–79（79 aa） Chain K 1–79（79 aa） Chain L 1–79（79 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；300 K；Ionic strength (raw mmCIF value) 50 mM；Pressure AMBIENT NMR measurement conditions pH 8；300 K；Ionic strength (raw mmCIF value) 50 mM；Pressure AMBIENT NMR sample composition 1 MM SUBUNIT C	Resolution not provided
1C99 ASP61 DEPROTONATED FORM OF SUBUNIT C OF THE F1FO ATP SYNTHASE OF ESCHERICHIA COLI Deposited 1999-04-30	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 1–79（79 aa） Fragment：subunit c	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；300 K	Resolution not provided
1IJP Solution Structure of Ala20Pro/Pro64Ala substituted subunit c of Escherichia coli ATP synthase Deposited 2001-04-27	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 1–79（79 aa） Fragment：subunit c	Mutation：A20P, P64A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；300 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure atmospheric NMR sample composition 2.2 mM subunit c, 50 mM NaCl, pH 5.0 \| CDCl3:CD3OD:D2O=4:4:1 or CDCl3:CD3OH:H2O=4:4:1	Resolution not provided
1L6T STRUCTURE OF ALA24/ASP61 TO ASP24/ASN61 SUBSTITUTED SUBUNIT C OF ESCHERICHIA COLI ATP SYNTHASE Deposited 2002-03-13	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 1–79（79 aa）	Mutation：A24D, D61N	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；300 K；Ionic strength (raw mmCIF value) 50 mM NACL；Pressure ATMOSPHERIC NMR sample composition 2.0 MM SUBUNIT C, 50 MM NACL, PH 5.0 \| CDCl3:CD3OH:H20=4:4:1	Resolution not provided

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

View Construct and Data Evidence

UniProt name	ATPL_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Z； PDBConstruct 1–79； UniProt 1–79

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	4utq
Deposition date deposition_date	2014-07-22
Structure title title	A structural model of the active ribosome-bound membrane protein insertase YidC
Keywords keywords	PROTEIN TRANSPORT, PROTEIN TRANSLOCATION, BIOINFORMATICS, MD SIMULATION, MEMBRANE; PROTEIN TRANSPORT
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	15.49 Å
Radius of gyration Rg (electron density) rg_electron	14.73 Å
Forward intensity I(0) i0	3080450.00
Molecular weight molecular_weight	7742.0 kDa
Excluded volume excluded_volume	7630 Å³
Envelope volume envelope_volume	14730 Å³
Hydration-shell volume shell_volume	9403 Å³
Envelope diameter envelope_diameter	47.9 Å
Shell Rg shell_rg	18.84 Å
Envelope Rg envelope_rg	14.06 Å
Shape Rg shape_rg	14.71 Å
Total Rg total_rg	15.52 Å
Total atoms total_atoms	552
Residues n_residues	138
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	48.0 Å
Rg (real space) rg_real	15.37 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	3.0800e+06
I(0) uncertainty (real space) i0_real_error	3.7470e+04
Rg (reciprocal space) rg_reciprocal	15.38 Å
I(0) (reciprocal space) i0_reciprocal	3080000.0000
Solution quality estimate total_estimate	0.7711
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	-0.001
Kurtosis Kurtosis kurtosis	-0.311
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	339200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.681; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	MEMBRANE PROTEIN INSERTASE YIDC
Molecular weight formula_weight	61576.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	552

MDSQRNLLVIALLFVSFMIWQAWEQDKNPQPQAQQTTQTTTTAAGSAADQGVPASGQGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLDTGSSNFALHTFRGAAYSTPDEKYEKYKFDTIADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVAPHLDLTVDYGWLWFISQPLFKLLKWIHSFVGNWGFSIIIITFIVRGIMYPLTKAQYTSMAKMRMLQPKIQAMRERLGDDKQRISQEMMALYKAEKVNPLGGCFPLLIQMPIFLALYYMLMGSVELRQAPFALWIHDLSAQDPYYILPILMGVTMFFIQKMSPTTVTDPMQQKIMTFMPVIFTVFFLWFPSGLVLYYIVSNLVTIIQQQLIYRGLEKRGLHSREKKKS

Entity 2 Entity 2 polymer

Description description	ATP SYNTHASE SUBUNIT C
Molecular weight formula_weight	8259.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

MENLNMDLLYMAAAVMMGLAAIGAAIGIGILGGKFLEGAARQPDLIPLLRTQFFIVMGLVDAIPMIAVGLGLYVMFAVA

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8. Citations (1)

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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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	8.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	8.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	58960

fit	/app/data/saxs_computation/ut/4utq/4utq.fit
pddf	/app/data/pr_computation/ut/4utq/4utq.pr.out
profile	/app/data/saxs_computation/ut/4utq/4utq.dat

A structural model of the active ribosome-bound membrane protein insertase YidC

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

MEMBRANE PROTEIN INSERTASE YIDC

State in the Current Structure

Other States of the Same Protein in the Database

ATP SYNTHASE SUBUNIT C

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)