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- PDB-6us8: Influenza A M2 proton channel wild type TM domain bound to S-rima... -

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Basic information

Entry
Database: PDB / ID: 6us8
TitleInfluenza A M2 proton channel wild type TM domain bound to S-rimantadine
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / proton channel / rimantadine
Function / homologyInfluenza virus matrix protein 2 / Influenza Matrix protein (M2) / proton transmembrane transporter activity / channel activity / host cell plasma membrane / virion membrane / membrane / Chem-EU7 / Matrix protein 2
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsThomaston, J.L. / DeGrado, W.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM122603 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM117593 United States
CitationJournal: Biochemistry / Year: 2021
Title: Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity.
Authors: Thomaston, J.L. / Samways, M.L. / Konstantinidi, A. / Ma, C. / Hu, Y. / Bruce Macdonald, H.E. / Wang, J. / Essex, J.W. / DeGrado, W.F. / Kolocouris, A.
History
DepositionOct 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein 2
B: Matrix protein 2
C: Matrix protein 2
D: Matrix protein 2
E: Matrix protein 2
F: Matrix protein 2
G: Matrix protein 2
H: Matrix protein 2
I: Matrix protein 2
J: Matrix protein 2
K: Matrix protein 2
L: Matrix protein 2
M: Matrix protein 2
N: Matrix protein 2
O: Matrix protein 2
P: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,36332
Polymers44,06916
Non-polymers2,29316
Water1,60389
1
A: Matrix protein 2
B: Matrix protein 2
C: Matrix protein 2
D: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4117
Polymers11,0174
Non-polymers3943
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-50 kcal/mol
Surface area5430 Å2
MethodPISA
2
E: Matrix protein 2
F: Matrix protein 2
G: Matrix protein 2
H: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4117
Polymers11,0174
Non-polymers3943
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-53 kcal/mol
Surface area5500 Å2
MethodPISA
3
I: Matrix protein 2
J: Matrix protein 2
K: Matrix protein 2
L: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7709
Polymers11,0174
Non-polymers7535
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-48 kcal/mol
Surface area5570 Å2
MethodPISA
4
M: Matrix protein 2
N: Matrix protein 2
O: Matrix protein 2
P: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7709
Polymers11,0174
Non-polymers7535
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-49 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.390, 76.090, 98.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 24 - 46 / Label seq-ID: 4 - 26

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A'AA
2(chain 'B' and resid 24 through 46)BB
3chain 'C'CC
4(chain 'D' and resid 24 through 46)DD
5chain 'E'EE
6(chain 'F' and resid 24 through 46)FF
7chain 'G'GG
8(chain 'H' and resid 24 through 46)HH
9(chain 'I' and resid 24 through 46)II
10(chain 'J' and resid 24 through 46)JJ
11(chain 'K' and resid 24 through 46)KK
12(chain 'L' and resid 24 through 46)LL
13(chain 'M' and resid 24 through 46)MM
14(chain 'N' and resid 24 through 46)NN
15chain 'O'OO
16chain 'P'PP

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Components

#1: Protein/peptide
Matrix protein 2


Mass: 2754.340 Da / Num. of mol.: 16 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/Jinfang/132/2002(H3N2))
References: UniProt: D5F6K1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EU7 / (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine / S-RIMANTADINE


Mass: 179.302 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H21N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 44.25 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: monoolein, 0.05 M HEPES pH 7.5, 22% w/vPEG 4000, 50 mM MNG-3-C8, S-rimantadine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.7→60.25 Å / Num. obs: 37869 / % possible obs: 91.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.4060983423 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.036 / Net I/σ(I): 11.3
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1950 / CC1/2: 0.872 / Rpim(I) all: 0.349

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Cootmodel building
Cootmodel building
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BKL

6bkl


Resolution: 1.7→60.25 Å / SU ML: 0.178426145769 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3344112615
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2142 2050 5.42801917018 %
Rwork0.1889 35717 -
obs0.1903 37767 90.6683631824 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.6450697009 Å2
Refinement stepCycle: LAST / Resolution: 1.7→60.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 136 89 3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.07045273079333313
X-RAY DIFFRACTIONf_angle_d2.716595958524608
X-RAY DIFFRACTIONf_chiral_restr1.90347925307670
X-RAY DIFFRACTIONf_plane_restr0.00644977129739477
X-RAY DIFFRACTIONf_dihedral_angle_d14.59195962061034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73960.27621310.23582315X-RAY DIFFRACTION90.3249630724
1.7396-1.78310.2273320547161340.2141903518542321X-RAY DIFFRACTION89.110707804
1.7831-1.83130.2510966498741310.1997974687792306X-RAY DIFFRACTION89.0390938984
1.8313-1.88520.2170940735051310.184407795512302X-RAY DIFFRACTION89.0882460637
1.8852-1.9460.2332745691861320.1654933453682291X-RAY DIFFRACTION88.0450581395
1.946-2.01560.2229724546831310.159674395092262X-RAY DIFFRACTION87.3357664234
2.0156-2.09630.1963076683691330.1580764548872280X-RAY DIFFRACTION88.1300219138
2.0963-2.19170.1670805864411310.1390667458542296X-RAY DIFFRACTION87.9985496737
2.1917-2.30720.1826928965661320.1428211720712281X-RAY DIFFRACTION87.0804763623
2.3072-2.45180.190479148581310.1577625479662294X-RAY DIFFRACTION87.355907781
2.4518-2.64110.1752328227391310.1698486445712305X-RAY DIFFRACTION88.3569096844
2.6411-2.90690.2038885387851430.1667840686072478X-RAY DIFFRACTION93.1745467472
2.9069-3.32750.2167497168261470.189123838112560X-RAY DIFFRACTION97.0250896057
3.3275-4.19210.2187962998091520.2114093537962649X-RAY DIFFRACTION98.5573539761
4.1921-60.24562944290.2435573847471600.2347590627462777X-RAY DIFFRACTION98.490945674

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