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- PDB-3lbw: High resolution crystal structure of transmembrane domain of M2 -

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Basic information

Entry
Database: PDB / ID: 3lbw
TitleHigh resolution crystal structure of transmembrane domain of M2
ComponentsM2 proteinM2 proton channel
KeywordsTRANSPORT PROTEIN / Proton channel / M2TM / Influenza A virus M2 protein / Host cell membrane / Hydrogen ion transport / Ionic channel / Transmembrane / Virion
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
DI(HYDROXYETHYL)ETHER / Xylitol / 4-bromobenzoic acid / Matrix protein 2 / Matrix protein 2
Similarity search - Component
Biological speciesinfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAcharya, R. / Polishchuk, A.L. / DeGrado, W.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus.
Authors: Acharya, R. / Carnevale, V. / Fiorin, G. / Levine, B.G. / Polishchuk, A.L. / Balannik, V. / Samish, I. / Lamb, R.A. / Pinto, L.H. / DeGrado, W.F. / Klein, M.L.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M2 protein
B: M2 protein
C: M2 protein
D: M2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,08712
Polymers9,8124
Non-polymers1,2758
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-39 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.665, 79.091, 48.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide
M2 protein / M2 proton channel


Mass: 2453.085 Da / Num. of mol.: 4 / Fragment: Transmembrane domain, residues 25-46 / Mutation: G34A / Source method: obtained synthetically / Source: (synth.) influenza A virus / References: UniProt: Q9YP62, UniProt: O70632*PLUS
#2: Chemical
ChemComp-Z82 / 4-bromobenzoic acid


Mass: 201.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5BrO2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Sugar ChemComp-XYL / Xylitol / D-Xylitol / Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H12O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 0.8mM M2TM (25-46) peptide (as monomer),28mM Octyl-beta-D-Glucopyranosie and 5% xylitol. Reservoir solution: 95% [100mM sodium citrate pH 5.6, 150mM tri-sodium citrate, 15% ...Details: Protein solution: 0.8mM M2TM (25-46) peptide (as monomer),28mM Octyl-beta-D-Glucopyranosie and 5% xylitol. Reservoir solution: 95% [100mM sodium citrate pH 5.6, 150mM tri-sodium citrate, 15% v/v isopropanol] and 5% [0.2M MgCl2 6H20, 0.1M Tris-Hcl pH 8.5, 30% w/v PEG 4000], VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9191 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2008
RadiationMonochromator: Monochromator: Si(111) channel cut monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 1.65→48.56 Å / Num. all: 11567 / Num. obs: 11509 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 15.278 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1599 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BKD, chain A

3bkd


Resolution: 1.65→31.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.665 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20529 554 4.8 %RANDOM
Rwork0.19621 ---
all0.207 10998 --
obs0.19664 10998 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.431 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.65→31.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms696 0 67 23 786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022775
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8662.0511034
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.858584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg53.9222016
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00415124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.336154
X-RAY DIFFRACTIONr_chiral_restr0.0540.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02468
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4551.5448
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8062716
X-RAY DIFFRACTIONr_scbond_it1.2293327
X-RAY DIFFRACTIONr_scangle_it2.0434.5318
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 38 -
Rwork0.284 750 -
obs--100 %

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