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- PDB-5cqe: 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1... -

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Basic information

Entry
Database: PDB / ID: 5cqe
Title2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from Influenza A virus (A/Puerto Rico/8/34(H1N1))
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / matrix protein 1 / Influenza A virus (A/Puerto Rico/8/34(H1N1)) / CSGID / virulence / pathogenesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral mRNA Translation / viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / extracellular region / plasma membrane
Similarity search - Function
Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix protein M1, N-terminal subdomain 2 / Influenza Virus Matrix Protein; Chain A, domain 1 / Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) ...Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix protein M1, N-terminal subdomain 2 / Influenza Virus Matrix Protein; Chain A, domain 1 / Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Matrix protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHalavaty, A.S. / Minasov, G. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Shuvalova, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from Influenza A virus (A/Puerto Rico/8/34(H1N1))
Authors: Halavaty, A.S. / Minasov, G. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Shuvalova, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein 1
B: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3018
Polymers41,9042
Non-polymers3976
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-29 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.367, 117.896, 40.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 0 - 157 / Label seq-ID: 24 - 181

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Matrix protein 1 / M1


Mass: 20952.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: P03485

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Non-polymers , 5 types, 96 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 12.8 mg/mL 10 mM Tris-HCl pH 8.3 500 mM NaCl 0.5 mM TCEP Crsytallization: The JCSG+ Suite (B9: 100 mM Citric acid pH 4.0 20% (w/v) PEG 6000; final pH 5.0 Cryocondition: ...Details: Protein: 12.8 mg/mL 10 mM Tris-HCl pH 8.3 500 mM NaCl 0.5 mM TCEP Crsytallization: The JCSG+ Suite (B9: 100 mM Citric acid pH 4.0 20% (w/v) PEG 6000; final pH 5.0 Cryocondition: Crystallization condition + sucrose (50%)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2015
RadiationMonochromator: DIAMOND[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 22646 / Num. obs: 22646 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 25.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
BLU-MAXdata collection
PHASERphasing
HKL-2000data reduction
Cootmodel building
ARPmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA3
Resolution: 2.1→29.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 8.136 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19745 1086 4.8 %RANDOM
Rwork0.17491 ---
obs0.17603 21413 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.391 Å2
Baniso -1Baniso -2Baniso -3
1-4.36 Å2-0 Å2-0 Å2
2---3.18 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.1→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 22 90 2563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192585
X-RAY DIFFRACTIONr_bond_other_d0.0050.022575
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9873498
X-RAY DIFFRACTIONr_angle_other_deg1.05435925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0035334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68624.02102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18315472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5881518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022914
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02562
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9200 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 74 -
Rwork0.231 1534 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.142-0.031-0.28763.8384-0.37881.0417-0.03450.08550.0717-0.18870.09-0.12330.15980.0484-0.05550.0356-0.0021-0.00030.21870.02810.24156.953412.328937.1574
21.72040.5423-0.02821.9226-0.99912.93730.0732-0.0010.33030.25210.0747-0.13280.07950.0166-0.14790.0639-0.0212-0.05150.1479-0.01840.162451.56888.45853.2694
31.0461-0.5414-0.30242.78220.13152.1590.02780.1437-0.1082-0.2298-0.035-0.06990.13070.02760.00720.02960.0150.0050.0996-0.03660.092250.8201-21.677437.4577
41.2098-0.30950.36872.92480.88272.5523-0.0484-0.1137-0.05320.18120.0789-0.13280.0360.1312-0.03060.013-0.0026-0.00390.117-0.00820.056252.2341-14.45152.8841
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 87
2X-RAY DIFFRACTION2A88 - 158
3X-RAY DIFFRACTION3B-1 - 76
4X-RAY DIFFRACTION4B77 - 159

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