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- PDB-3bkd: High resolution Crystal structure of Transmembrane domain of M2 p... -

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Basic information

Entry
Database: PDB / ID: 3bkd
TitleHigh resolution Crystal structure of Transmembrane domain of M2 protein
ComponentsTransmembrane Domain of Matrix protein M2
KeywordsVIRAL PROTEIN / MEMBRANE PROTEIN / Proton channel / M2TM / Influenza A virus M2 Protein
Function / homology
Function and homology information


suppression by virus of host autophagy / : / proton transmembrane transporter activity / : / protein complex oligomerization / monoatomic ion channel activity / membrane => GO:0016020 / host cell plasma membrane / virion membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Matrix protein 2
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsStouffer, A.L. / Acharya, R. / Salom, D.
CitationJournal: Nature / Year: 2008
Title: Structural basis for the function and inhibition of an influenza virus proton channel
Authors: Stouffer, A.L. / Acharya, R. / Salom, D. / Levine, A.S. / Di Costanzo, L. / Soto, C.S. / Tereshko, V. / Nanda, V. / Stayrook, S. / DeGrado, W.F.
History
DepositionDec 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane Domain of Matrix protein M2
B: Transmembrane Domain of Matrix protein M2
C: Transmembrane Domain of Matrix protein M2
D: Transmembrane Domain of Matrix protein M2
E: Transmembrane Domain of Matrix protein M2
F: Transmembrane Domain of Matrix protein M2
G: Transmembrane Domain of Matrix protein M2
H: Transmembrane Domain of Matrix protein M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,80822
Polymers22,3468
Non-polymers2,46214
Water70339
1
E: Transmembrane Domain of Matrix protein M2
F: Transmembrane Domain of Matrix protein M2
G: Transmembrane Domain of Matrix protein M2
H: Transmembrane Domain of Matrix protein M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,29810
Polymers11,1734
Non-polymers1,1256
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-33 kcal/mol
Surface area7710 Å2
MethodPISA
2
A: Transmembrane Domain of Matrix protein M2
B: Transmembrane Domain of Matrix protein M2
C: Transmembrane Domain of Matrix protein M2
D: Transmembrane Domain of Matrix protein M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,51012
Polymers11,1734
Non-polymers1,3378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-25 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.753, 56.557, 56.009
Angle α, β, γ (deg.)90.00, 103.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: NH2 / End label comp-ID: NH2 / Refine code: 6 / Auth seq-ID: 22 - 47 / Label seq-ID: 1 - 26

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21EE
12BB
22FF
13CC
23GG
14DD
24HH

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein/peptide
Transmembrane Domain of Matrix protein M2


Mass: 2793.236 Da / Num. of mol.: 8 / Fragment: residues 22-46 / Source method: obtained synthetically
Details: Chemically synthesized; Transmembrane domain of M2 protein from Influenza A virus
References: UniProt: Q9Q0P0
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Protein solution: 0.8mM protein, 32mM n-octyl-beta-D-glucopyranoside and 5%v/v xylitol. Reservoir solution: 50mM Tris-Hcl, 500mM MgCl2, 21% PEG 350 MME, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2001
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 15355 / Num. obs: 14567 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 1.9 / Num. unique all: 777 / % possible all: 75.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Amantandine-bound M2TM; G34A mutant

Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.819 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26871 747 5 %RANDOM
Rwork0.21908 ---
all0.244 ---
obs0.22158 14047 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.04 Å2
2--2.17 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 164 39 1747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221741
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3482.0812328
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4245192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1952240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96615294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.918158
X-RAY DIFFRACTIONr_chiral_restr0.080.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021032
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.2793
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21216
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4990.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8871.51058
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14721618
X-RAY DIFFRACTIONr_scbond_it1.6623799
X-RAY DIFFRACTIONr_scangle_it2.2894.5710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A190loose positional0.275
2B193loose positional0.375
3C189loose positional0.295
4D189loose positional0.325
1A190loose thermal2.7610
2B193loose thermal1.2910
3C189loose thermal0.8710
4D189loose thermal1.3410
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 53 -
Rwork0.217 992 -
obs--96.67 %
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)
10.1613-0.2459-0.51970.9080.55491.78010.0721-0.0472-0.01380.09510.0106-0.0882-0.10840.0771-0.08260-0.010.0017-0.013-0.00150.0320.147915.7169-0.9902
20.2352-0.101-0.67261.0747-0.47432.48810.0279-0.039-0.0272-0.0490.00320.04770.1355-0.0729-0.0311-0.00180.0143-0.01890.03210.0073-0.01267.024311.4201-28.1435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 461 - 25
2X-RAY DIFFRACTION1BB22 - 461 - 25
3X-RAY DIFFRACTION1CC22 - 461 - 25
4X-RAY DIFFRACTION1DD22 - 461 - 25
5X-RAY DIFFRACTION2EE22 - 461 - 25
6X-RAY DIFFRACTION2FF22 - 461 - 25
7X-RAY DIFFRACTION2GG22 - 461 - 25
8X-RAY DIFFRACTION2HH22 - 461 - 25

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