6N7G

Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form I)

PDB DOI: https://doi.org/10.2210/pdb6N7G/pdb
EM Map EMD-0355: EMDB EMDataResource

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2018-11-27 Released: 2019-05-29
Deposition Author(s): Yan, N., Gong, X., Qian, H.W.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 650.74 kDa
Atom Count: 34,484
Modelled Residue Count: 4,306
Deposited Residue Count: 5,744
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein patched homolog 1	A, B, D, E	1,349	Homo sapiens	Mutation(s): 0 Gene Names: PTCH1, PTCH Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q13635 (Homo sapiens) Explore Q13635 Go to UniProtKB: Q13635
PHAROS: Q13635 GTEx: ENSG00000185920
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13635
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sonic hedgehog protein	C, F	174	Homo sapiens	Mutation(s): 0 Gene Names: SHH Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q15465 (Homo sapiens) Explore Q15465 Go to UniProtKB: Q15465
PHAROS: Q15465 GTEx: ENSG00000164690
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15465
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain RA [auth F] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain KA [auth D] SDF format, chain QA [auth E] SDF format, chain R [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth A]	IA [auth D] JA [auth D] KA [auth D] P [auth A] Q [auth A] IA [auth D], JA [auth D], KA [auth D], P [auth A], Q [auth A], QA [auth E], R [auth A], RA [auth F], X [auth B], Y [auth C]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth F] Focus chain X [auth B] Focus chain Y [auth C] Interactions & Density Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth F] Focus chain X [auth B] Focus chain Y [auth C]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain VA [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain VA [auth F]	CA [auth C], VA [auth F]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain VA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain VA [auth F]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain K [auth A] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain PA [auth E] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	DA [auth D] EA [auth D] FA [auth D] GA [auth D] HA [auth D] DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], K [auth A], L [auth A], LA [auth E], M [auth A], MA [auth E], N [auth A], NA [auth E], O [auth A], OA [auth E], PA [auth E], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain SA [auth F] SDF format, chain Z [auth C] MOL2 format, chain SA [auth F] MOL2 format, chain Z [auth C]	SA [auth F], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain SA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain SA [auth F] Focus chain Z [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain TA [auth F] SDF format, chain UA [auth F] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain TA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain BA [auth C]	AA [auth C], BA [auth C], TA [auth F], UA [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain TA [auth F] Focus chain UA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain TA [auth F] Focus chain UA [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-29

Deposition Author(s):

Yan, N.

Gong, X.

Qian, H.W.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DMR-1420541

Revision History (Full details and data files)

Version 1.0: 2019-05-29
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence
Version 1.2: 2019-12-18
Changes: Database references, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary