3J8F

Cryo-EM reconstruction of poliovirus-receptor complex

• PDB DOI: https://doi.org/10.2210/pdb3J8F/pdb
• EM Map EMD-6147: EMDB EMDataResource

• Classification: VIRUS/SIGNALING PROTEIN
• Organism(s): Human poliovirus 1 Mahoney, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-20 Released: 2015-02-11 
• Deposition Author(s): Strauss, M., Filman, D.J., Belnap, D.M., Cheng, N., Noel, R.T., Hogle, J.M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 300-mer - A60B60C60D60E60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 300-mer - A120B60C60D60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 147.75 kDa 
• Atom Count: 9,263 
• Modelled Residue Count: 1,160 
• Deposited Residue Count: 1,304 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A [auth 1]	302	Human poliovirus 1 Mahoney	Mutation(s): 0
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney)) Explore P03300  Go to UniProtKB:  P03300

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP2	B [auth 2]	272	Human poliovirus 1 Mahoney	Mutation(s): 0
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney)) Explore P03300  Go to UniProtKB:  P03300

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C [auth 3]	238	Human poliovirus 1 Mahoney	Mutation(s): 0
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney)) Explore P03300  Go to UniProtKB:  P03300

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP4	D [auth 4]	69	Human poliovirus 1 Mahoney	Mutation(s): 1
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney)) Explore P03300  Go to UniProtKB:  P03300

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Poliovirus receptor	E [auth 7]	423	Homo sapiens	Mutation(s): 0  Gene Names: PVR, PVS
UniProt & NIH Common Fund Data Resources
Find proteins for P15151 (Homo sapiens) Explore P15151  Go to UniProtKB:  P15151
PHAROS:  P15151 GTEx:  ENSG00000073008

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth A], J [auth E]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth B]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G51347YJ GlyCosmos:  G51347YJ GlyGen:  G51347YJ

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth C], I [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth F]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth 7]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	RELION	1.2

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Strauss, M., Filman, D.J., Belnap, D.M., Cheng, N., Noel, R.T., Hogle, J.M.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2022-12-21
  Changes: Database references, Derived calculations, Refinement description, Structure summary