6NM5

F-pilus/MS2 Maturation protein complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis for the adsorption of a single-stranded RNA bacteriophage.

Meng, R., Jiang, M., Cui, Z., Chang, J.Y., Yang, K., Jakana, J., Yu, X., Wang, Z., Hu, B., Zhang, J.

(2019) Nat Commun 10: 3130-3130

  • DOI: 10.1038/s41467-019-11126-8
  • Primary Citation of Related Structures:  
    6NM5

  • PubMed Abstract: 

    • Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus, showing a network of hydrophobic and electrostatic interactions at the Mat-pilus interface ...

    Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus, showing a network of hydrophobic and electrostatic interactions at the Mat-pilus interface. Moreover, binding of the pilus induces slight orientational variations of the Mat relative to the rest of the phage capsid, priming the Mat-connected genomic RNA (gRNA) for its release from the virions. The exposed tip of the attached Mat points opposite to the direction of the pilus retraction, which may facilitate the translocation of the gRNA from the capsid into the host cytosol. In addition, our structures determine the orientation of the assembled F-pilin subunits relative to the cell envelope, providing insights into the F-like type IV secretion systems.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA. junjiez@tamu.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type IV conjugative transfer system pilin TraA65Escherichia coliMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Maturation proteinXB [auth M]393Emesvirus zinderiMutation(s): 0 
Gene Names: A
UniProt
Find proteins for P03610 (Escherichia phage MS2)
Explore P03610 
Go to UniProtKB:  P03610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03610
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KSV
Query on KSV
Download Ideal Coordinates CCD File 
AC [auth 1B],
AD [auth 2M],
AE [auth 4L],
BC [auth 1C],
BD [auth 2N],
AC [auth 1B],
AD [auth 2M],
AE [auth 4L],
BC [auth 1C],
BD [auth 2N],
BE [auth 4M],
CC [auth 1D],
CD [auth 3A],
CE [auth 4N],
DC [auth 1F],
DD [auth 3A],
DE [auth 5A],
EC [auth 1F],
ED [auth 3B],
EE [auth 5C],
FC [auth 1G],
FD [auth 3C],
FE [auth 5D],
GC [auth 1H],
GD [auth 3D],
GE [auth 5E],
HC [auth 1I],
HD [auth 3E],
HE [auth 5G],
IC [auth 1J],
ID [auth 3G],
IE [auth 5H],
JC [auth 1J],
JD [auth 3H],
JE [auth 5I],
KC [auth 1K],
KD [auth 3I],
KE [auth 5I],
LC [auth 1K],
LD [auth 3J],
LE [auth 5J],
MC [auth 1L],
MD [auth 3K],
ME [auth 5K],
NC [auth 1M],
ND [auth 3K],
NE [auth 5L],
OC [auth 1N],
OD [auth 3L],
OE [auth 5M],
PC [auth 2B],
PD [auth 3M],
PE [auth 5N],
QC [auth 2C],
QD [auth 3N],
RC [auth 2D],
RD [auth 4A],
SC [auth 2E],
SD [auth 4B],
TC [auth 2E],
TD [auth 4C],
UC [auth 2F],
UD [auth 4D],
VC [auth 2G],
VD [auth 4E],
WC [auth 2H],
WD [auth 4F],
XC [auth 2I],
XD [auth 4F],
YB [auth 1A],
YC [auth 2J],
YD [auth 4G],
ZB [auth 1B],
ZC [auth 2L],
ZD [auth 4H]
(2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate
C5 H13 O6 P
DXARXEBAXKHIOU-RXMQYKEDSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP41GM103832
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesU24GM1167

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other