1JMU | pdb_00001jmu

Crystal Structure of the Reovirus mu1/sigma3 Complex

PDB DOI: https://doi.org/10.2210/pdb1JMU/pdb

Classification: VIRAL PROTEIN
Organism(s): Reovirus sp.
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2001-07-20 Released: 2002-02-06
Deposition Author(s): Liemann, S., Nibert, M.L., Harrison, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure of the reovirus membrane-penetration protein, Mu1, in a complex with is protector protein, Sigma3.

Liemann, S., Chandran, K., Baker, T.S., Nibert, M.L., Harrison, S.C.

(2002) Cell 108: 283-295

PubMed: 11832217 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/s0092-8674(02)00612-8
Primary Citation Related Structures:
1JMU

PubMed Abstract:
Cell entry by nonenveloped animal viruses requires membrane penetration without membrane fusion. The reovirus penetration agent is the outer-capsid protein, Mu1. The structure of Mu1, complexed with its "protector" protein, Sigma3, and the fit of this Mu1(3)Sigma3(3) heterohexameric complex into the cryoEM image of an intact virion, reveal molecular events essential for viral penetration. Autolytic cleavage divides Mu1 into myristoylated Mu1N and Mu1C. A long hydrophobic pocket can receive the myristoyl group. Dissociation of Mu1N, linked to a major conformational change of the entire Mu1 trimer, must precede myristoyl-group insertion into the cellular membrane. A myristoyl switch, coupling exposure of the fatty acid chain, autolytic cleavage of Mu1N, and long-range molecular rearrangement of Mu1C, thus appears to be part of the penetration mechanism.

Organizational Affiliation

Howard Hughes Medical Institute, Children's Hospital, Harvard Medical School, 320 Longwood Avenue, Boston, MA 02115, USA.

Macromolecule Content

Total Structure Weight: 354.46 kDa
Atom Count: 23,657
Modeled Residue Count: 3,021
Deposited Residue Count: 3,219
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN MU-1	A, C, E	41	Reovirus sp.	Mutation(s): 0 Gene Names: M2
UniProt
Find proteins for P11077 (Reovirus type 1 (strain Lang)) Explore P11077 Go to UniProtKB: P11077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11077
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN MU-1	B, D, F	666	Reovirus sp.	Mutation(s): 0 Gene Names: M2
UniProt
Find proteins for P11077 (Reovirus type 1 (strain Lang)) Explore P11077 Go to UniProtKB: P11077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11077
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGMA 3 PROTEIN	G, H, I	366	Reovirus sp.	Mutation(s): 1 Gene Names: S4
UniProt
Find proteins for P07939 (Reovirus type 1 (strain Lang)) Explore P07939 Go to UniProtKB: P07939
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07939
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain M [auth D] SDF format, chain K [auth B] MOL2 format, chain O [auth F] MOL2 format, chain M [auth D] MOL2 format, chain K [auth B] mmCIF format, chain O [auth F] mmCIF format, chain M [auth D] mmCIF format, chain K [auth B]	K [auth B], M [auth D], O [auth F]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain K [auth B] Focus chain M [auth D] Focus chain O [auth F] Interactions & Density Focus chain K [auth B] Focus chain M [auth D] Focus chain O [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth I] SDF format, chain X [auth I] SDF format, chain V [auth H] SDF format, chain U [auth H] SDF format, chain S [auth G] SDF format, chain R [auth G] SDF format, chain P [auth F] SDF format, chain N [auth D] SDF format, chain L [auth B] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth I] MOL2 format, chain V [auth H] MOL2 format, chain U [auth H] MOL2 format, chain S [auth G] MOL2 format, chain R [auth G] MOL2 format, chain P [auth F] MOL2 format, chain N [auth D] MOL2 format, chain L [auth B] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth I] mmCIF format, chain V [auth H] mmCIF format, chain U [auth H] mmCIF format, chain S [auth G] mmCIF format, chain R [auth G] mmCIF format, chain P [auth F] mmCIF format, chain N [auth D] mmCIF format, chain L [auth B]	L [auth B] N [auth D] P [auth F] R [auth G] S [auth G] L [auth B], N [auth D], P [auth F], R [auth G], S [auth G], U [auth H], V [auth H], X [auth I], Y [auth I]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth B] Focus chain N [auth D] Focus chain P [auth F] Focus chain R [auth G] Focus chain S [auth G] Focus chain U [auth H] Focus chain V [auth H] Focus chain X [auth I] Focus chain Y [auth I] Interactions & Density Focus chain L [auth B] Focus chain N [auth D] Focus chain P [auth F] Focus chain R [auth G] Focus chain S [auth G] Focus chain U [auth H] Focus chain V [auth H] Focus chain X [auth I] Focus chain Y [auth I]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Q [auth G] SDF format, chain T [auth H] SDF format, chain W [auth I] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth H] MOL2 format, chain W [auth I] mmCIF format, chain Q [auth G] mmCIF format, chain T [auth H] mmCIF format, chain W [auth I]	Q [auth G], T [auth H], W [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth G] Focus chain T [auth H] Focus chain W [auth I] Interactions & Density Focus chain Q [auth G] Focus chain T [auth H] Focus chain W [auth I]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.241 (Depositor), 0.240 (DCC)
R-Value Work: 0.216 (Depositor), 0.216 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.294	α = 90
b = 184.942	β = 90
c = 284.324	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-02-06

Deposition Author(s):

Liemann, S.

Nibert, M.L.

Harrison, S.C.

Revision History (Full details and data files)

Version 1.0: 2002-02-06
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2021-10-27
Changes: Database references, Structure summary
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary