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- PDB-6mpn: Racemic M2-TM I42E crystallized from racemic detergent -

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Basic information

Entry
Database: PDB / ID: 6mpn
TitleRacemic M2-TM I42E crystallized from racemic detergent
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / transmembrane / racemic / coiled-coil
Function / homology
Function and homology information


suppression by virus of host autophagy / proton transmembrane transporter activity / : / protein complex oligomerization / monoatomic ion channel activity / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsKreitler, D.F. / Yao, Z. / Mortenson, D.E. / Forest, K.T. / Gellman, S.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM061238 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM00839 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM08293 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: A Hendecad Motif Is Preferred for Heterochiral Coiled-Coil Formation.
Authors: Kreitler, D.F. / Yao, Z. / Steinkruger, J.D. / Mortenson, D.E. / Huang, L. / Mittal, R. / Travis, B.R. / Forest, K.T. / Gellman, S.H.
History
DepositionOct 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Matrix protein 2
A: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5754
Polymers4,9902
Non-polymers5852
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: heterochiral coiled-coil dimer forms across crystallographic inversion center
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-3 kcal/mol
Surface area4520 Å2
2
B: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7872
Polymers2,4951
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7872
Polymers2,4951
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)14.680, 37.250, 43.220
Angle α, β, γ (deg.)107.410, 96.730, 97.660
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide Matrix protein 2 / Proton channel protein M2


Mass: 2495.078 Da / Num. of mol.: 2 / Fragment: residues 25-46 / Mutation: I42E, G34A / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: O70632
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→18.335 Å / Num. obs: 14625 / % possible obs: 86.81 % / Redundancy: 3.8 % / Biso Wilson estimate: 48.35 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.03904 / Rrim(I) all: 0.07657 / Rsym value: 0.06578 / Net I/σ(I): 10.08
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.81 / Num. unique obs: 746 / CC1/2: 0.839 / Rpim(I) all: 0.3895 / Rrim(I) all: 0.7511 / Rsym value: 0.6401 / % possible all: 43.45

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→18.335 Å / SU ML: 0.01 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 731 5 %
Rwork0.2303 13884 -
obs0.2306 14615 86.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.15 Å2 / Biso mean: 30.2151 Å2 / Biso min: 9.99 Å2
Refinement stepCycle: final / Resolution: 1.4→18.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms356 0 96 5 457
Biso mean--88.3 45.72 -
Num. residues----48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3999-1.5080.2893860.28421654174052
1.508-1.65960.2771550.24892955311092
1.6596-1.89960.21681610.22613044320596
1.8996-2.39240.2331640.20723105326997
2.3924-18.33690.23341650.23513126329198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.25211.2995-0.09633.3553-0.95452.31150.0714-0.1771-0.15750.1581-0.02770.11380.10680.0010.11630.1169-0.0278-0.01660.1297-0.01750.1076-0.346.250620.9986
26.8682-3.58525.17975.0568-3.60376.90490.02590.22280.1672-0.1487-0.05310.0442-0.06160.07660.05380.0875-0.04220.01910.1141-0.01970.0744-2.76675.29530.144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 25 through 46 )B25 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 46 )A25 - 46

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