SAXSdb — 9ms8

▼

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

Protein patched homolog 1

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–618 Chain A； UniProt 721–1188	Not recorded	6H3 Fab light chain × 1 6H3 Fab heavy chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.73 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 9MS8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6DMB Cryo-EM structure of human Ptch1 Deposited 2018-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6DMO Cryo-EM structure of human Ptch1 with three mutations L282Q/T500F/P504L Deposited 2018-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1305（1305 aa）	Mutation：L282Q, T500F, P504L	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6DMY Cryo-EM structure of human Ptch1 and ShhN complex Deposited 2018-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 2 SER SERINE × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6E1H Structure of 2:1 human Ptch1-Shh-N complex Deposited 2018-07-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1447（1447 aa） Chain B 1–1447（1447 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2 PLM PALMITIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 3.50 Å
6N7G Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form I) Deposited 2018-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–1305（1305 aa） Chain B 1–1305（1305 aa） Chain D 1–1305（1305 aa） Chain E 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 CLR CHOLESTEROL × 10 ZN ZINC ION × 2 CA CALCIUM ION × 4 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.80 Å
6N7H Cryo-EM structure of the 2:1 hPtch1-Shhp complex Deposited 2018-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1305（1305 aa） Chain B 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CLR CHOLESTEROL × 5 ZN ZINC ION × 1 CA CALCIUM ION × 2 PLM PALMITIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6N7K Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form II) Deposited 2018-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–1305（1305 aa） Chain B 1–1305（1305 aa） Chain D 1–1305（1305 aa） Chain E 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 CLR CHOLESTEROL × 10 ZN ZINC ION × 2 CA CALCIUM ION × 4 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
6OEU Structure of human Patched1 Deposited 2019-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1447（1447 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 3.50 Å
6OEV Structure of human Patched1 in complex with native Sonic Hedgehog Deposited 2019-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1447（1447 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 3.80 Å
6RMG Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II Deposited 2019-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1189（1189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 11 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6RTW Crystal structure of the Patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and cholesterol-hemisuccinate Deposited 2019-05-27	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 136–423（288 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 Y01 CHOLESTEROL HEMISUCCINATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES/MOPS pH 7.5, 0.03 M of each halide (sodium fluoride, sodium bromide, sodium iodide), 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350	Resolution 1.90 Å R-free 0.230
6RTX Crystal structure of the Patched-1 (PTCH1) ectodomain 1 Deposited 2019-05-27	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 139–428（290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M bicine/Trizma base pH 8.5, 0.03M of each ethylene glycol (diethyleneglycol, triethyleneglycol, tetraethyleneglycol and pentaethyleneglycol), 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350	Resolution 1.95 Å R-free 0.257
6RTY Crystal structure of the Patched ectodomain in complex with nanobody NB64 Deposited 2019-05-27	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 136–423（288 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES/imidazole pH 6.5, 0.02M of each amino acid (L-glutamate, alanine, glycine, lysine, serine), 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350	Resolution 2.10 Å R-free 0.255
6RVC Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75 Deposited 2019-05-31	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 772–1023（252 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M sodium nitrate, 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.241
6RVC Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75 Deposited 2019-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 772–1023（252 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M sodium nitrate, 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.241
6RVC Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75 Deposited 2019-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 772–1023（252 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M sodium nitrate, 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.241
6RVD Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex Deposited 2019-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1447（1447 aa） Chain B 1–1447（1447 aa）	Not recorded	CLR CHOLESTEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 PLM PALMITIC ACID × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 0.06% Digitonin, 1mM CaCl2. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	PTC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–618； UniProt 1–618 Author chain A； PDBConstruct 619–1086； UniProt 721–1188

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	9ms8
Deposition date deposition_date	2025-01-09
Structure title title	PTCH1 in complex with Fab6H3
Keywords keywords	PTCH1, Antibody, hedgehog signaling, cryo-EM, membrane protein., MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	39.24 Å
Radius of gyration Rg (electron density) rg_electron	39.09 Å
Forward intensity I(0) i0	241164000.00
Molecular weight molecular_weight	131750.0 kDa
Excluded volume excluded_volume	167040 Å³
Envelope volume envelope_volume	221520 Å³
Hydration-shell volume shell_volume	48421 Å³
Envelope diameter envelope_diameter	132.7 Å
Shell Rg shell_rg	43.29 Å
Envelope Rg envelope_rg	39.09 Å
Shape Rg shape_rg	39.05 Å
Total Rg total_rg	39.51 Å
Total atoms total_atoms	9290
Residues n_residues	1189
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	127.6 Å
Rg (real space) rg_real	39.37 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	2.4120e+08
I(0) uncertainty (real space) i0_real_error	3.8590e+06
Rg (reciprocal space) rg_reciprocal	39.30 Å
I(0) (reciprocal space) i0_reciprocal	241100000.0000
Solution quality estimate total_estimate	0.8727
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.3 Å
Skewness Skewness skewness	0.342
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35900000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.624

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein patched homolog 1
Molecular weight formula_weight	122175.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9290

MASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGLRRAAAPDRDYLHRPSYCDAAFALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCGKFLVVGLLIFGAFAVGLKAANLETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTTEALLQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQIIEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWEEMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVLSFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLRWDCSKSQGAVGLAGVLLVALSVAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLAHAFSETGQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAVVVVFNFAMVLLIFPAILSMDLYRREDRRLDIFCCFTSPCHCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLGLLGVSLYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLLYDLHRSFSNVKYVMLEENKQLPKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDDGVLAYKLLVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQANIRPHRPEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICSNYTSLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMVLALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLALEHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFGPYPEVSPANDYKDDDDK

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	6H3 Fab light chain
Molecular weight formula_weight	10968.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

VLTQSPAIMSASLGERVTLTCTASSSVTSSYLHWYQQKPGSSPKLWIYSTSNLPFGVSPRFSGSGSGTSFSLTISSMEAEDAATYYCHQFHRSPYTFGGGTK

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	6H3 Fab heavy chain
Molecular weight formula_weight	12267.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVESGGGLVKPGGSRKLSCVASGFTLSDYGMHWVRQAPEKGLEWVAYIGSDSYTIYHADTMKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCGRNYGMDYWGQGTS

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

▶

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	3.73 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	258693

fit	/app/data/saxs_computation/ms/9ms8/9ms8.fit
pddf	/app/data/pr_computation/ms/9ms8/9ms8.pr.out
profile	/app/data/saxs_computation/ms/9ms8/9ms8.dat

PTCH1 in complex with Fab6H3

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

Protein patched homolog 1

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 (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)