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- PDB-8h3c: Crystal structure of M2e Influenza peptide in complex with antibo... -

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Basic information

Entry
Database: PDB / ID: 8h3c
TitleCrystal structure of M2e Influenza peptide in complex with antibody scFv
Components
  • Matrix protein 2
  • Single Chain Variable FragmentSingle-chain variable fragment
KeywordsANTIVIRAL PROTEIN / Single chain variable fragment
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 speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsKumar, U. / Madni, Z.K. / Gaur, V. / Salunke, D.M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: J.Biomed.Sci. / Year: 2023
Title: A structure and knowledge-based combinatorial approach to engineering universal scFv antibodies against influenza M2 protein.
Authors: Kumar, U. / Goyal, P. / Madni, Z.K. / Kamble, K. / Gaur, V. / Rajala, M.S. / Salunke, D.M.
History
DepositionOct 8, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond / pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single Chain Variable Fragment
B: Single Chain Variable Fragment
C: Single Chain Variable Fragment
D: Single Chain Variable Fragment
E: Single Chain Variable Fragment
F: Matrix protein 2
G: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)139,1367
Polymers139,1367
Non-polymers00
Water0
1
A: Single Chain Variable Fragment


Theoretical massNumber of molelcules
Total (without water)27,1291
Polymers27,1291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Single Chain Variable Fragment
F: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)28,8742
Polymers28,8742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Single Chain Variable Fragment


Theoretical massNumber of molelcules
Total (without water)27,1291
Polymers27,1291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Single Chain Variable Fragment
G: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)28,8742
Polymers28,8742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Single Chain Variable Fragment


Theoretical massNumber of molelcules
Total (without water)27,1291
Polymers27,1291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.818, 120.398, 176.858
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-IDDetails
d_1ens_1(chain "A" and (resid 6 through 7 or (resid 8...
d_2ens_1(chain "B" and (resid 6 through 7 or (resid 8...
d_3ens_1(chain "C" and (resid 6 through 7 or (resid 8...
d_4ens_1(chain "D" and (resid 6 through 7 or (resid 8...
d_5ens_1(chain "E" and (resid 6 through 32 or (resid 33...
d_1ens_2(chain "F" and (resid 2 through 10 or (resid 11...
d_2ens_2(chain "G" and (resid 2 through 3 or (resid 4...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LEULEUGLYGLYAA6 - 116 - 11
d_12ens_1LEULEUVALVALAA13 - 11613 - 116
d_13ens_1ASPASPILEILEAA135 - 240135 - 240
d_21ens_1LEULEUGLYGLYBB6 - 116 - 11
d_22ens_1LEULEUVALVALBB13 - 11613 - 116
d_23ens_1ASPASPILEILEBB135 - 240135 - 240
d_31ens_1LEULEUGLYGLYCC6 - 116 - 11
d_32ens_1LEULEUVALVALCC13 - 11613 - 116
d_33ens_1ASPASPILEILECC135 - 240135 - 240
d_41ens_1LEULEUGLYGLYDD6 - 116 - 11
d_42ens_1LEULEUVALVALDD13 - 11613 - 116
d_43ens_1ASPASPILEILEDD135 - 240135 - 240
d_51ens_1LEULEUILEILEEE6 - 2406 - 240
d_11ens_2SERSERILEILEFF2 - 111 - 10
d_21ens_2SERSERILEILEGG2 - 111 - 10

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.675508695397, -0.248052497631, 0.694375950665), (0.30269923928, 0.951994299837, 0.0456072759299), (-0.672354945682, 0.179378960576, 0.718165729842)-27.6165714045, 1.2320744657, 46.8806259505
2given(-0.99818801766, 0.00204173180597, -0.0601374486582), (-0.00669003180382, -0.996993560979, 0.0771950959697), (-0.0597990374032, 0.0774575412632, 0.995200685504)12.5273025454, -59.8395520284, 2.65598956557
3given(-0.56353809086, 0.254231069217, -0.78599706335), (-0.268533867453, -0.956169870382, -0.1167421989), (-0.781226204233, 0.145278155337, 0.607107795537)18.7869888411, -57.7647235366, 51.8678452183
4given(-0.737563254571, -0.287887053881, -0.610836712808), (-0.28590965243, 0.952624010763, -0.103745673478), (0.611764755567, 0.098125115672, -0.784930153275)45.6113430526, -10.4289863571, 69.041577784
5given(0.783468376371, -0.344137042761, -0.517442749516), (0.574377173059, 0.718856316839, 0.391581995001), (0.237209119334, -0.603999413526, 0.760865653164)19.4460339346, -24.7592141855, -2.6161934486

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Components

#1: Antibody
Single Chain Variable Fragment / Single-chain variable fragment


Mass: 27129.166 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Matrix protein 2 / Proton channel protein M2


Mass: 1744.919 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: N-terminal M2 protein peptide
Source: (synth.) Influenza A virus (A/New York/392/2004(H3N2))
References: UniProt: P0DOF5

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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: 4.01 Å3/Da / Density % sol: 69.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium Citrate Dibasic pH 5.2, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.42→60.2 Å / Num. obs: 30668 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 77.15 Å2 / CC1/2: 0.983 / Net I/σ(I): 6.7
Reflection shellResolution: 3.42→3.48 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1527 / CC1/2: 0.685

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DSI

6dsi


Resolution: 3.43→60.2 Å / SU ML: 0.3406 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3125
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 1472 4.8 %
Rwork0.2041 29176 -
obs0.2056 30648 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.36 Å2
Refinement stepCycle: LAST / Resolution: 3.43→60.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8520 0 0 0 8520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00268692
X-RAY DIFFRACTIONf_angle_d0.619111786
X-RAY DIFFRACTIONf_chiral_restr0.04421312
X-RAY DIFFRACTIONf_plane_restr0.00411510
X-RAY DIFFRACTIONf_dihedral_angle_d3.64741231
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.895797464756
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.592182220716
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.864645364967
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.997581544776
ens_2d_2FX-RAY DIFFRACTIONTorsion NCS3.29151374878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.43-3.540.30961200.27062636X-RAY DIFFRACTION99.78
3.54-3.660.29791530.25422594X-RAY DIFFRACTION99.93
3.66-3.810.27461210.25342625X-RAY DIFFRACTION99.78
3.81-3.980.26891240.21422614X-RAY DIFFRACTION99.74
3.98-4.190.2451500.19512628X-RAY DIFFRACTION99.75
4.2-4.460.21091330.17232618X-RAY DIFFRACTION99.49
4.46-4.80.20571320.16842639X-RAY DIFFRACTION99.93
4.8-5.280.18411360.16522646X-RAY DIFFRACTION99.61
5.28-6.050.21161280.19242659X-RAY DIFFRACTION99.75
6.05-7.620.23581300.23042722X-RAY DIFFRACTION99.72
7.62-60.20.23431450.20782795X-RAY DIFFRACTION99.06

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