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- PDB-4lp7: Crystal structure of the human metapneumovirus matrix protein -

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Basic information

Entry
Database: PDB / ID: 4lp7
TitleCrystal structure of the human metapneumovirus matrix protein
ComponentsMatrix protein M
KeywordsCALCIUM BINDING PROTEIN / twisted beta sandwich / viral matrix / lipid binding
Function / homology
Function and homology information


virion assembly / viral envelope / host cell plasma membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
HRSV-S2 matrix protein, N-terminal domain / Pneumovirus matrix protein / Pneumovirus matrix, N-terminal / Pneumovirus matrix protein / Topoisomerase I; domain 3 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman metapneumovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.83 Å
AuthorsLeyrat, C. / Harlos, K. / Grimes, J.M.
CitationJournal: Structure / Year: 2014
Title: Structure and self-assembly of the calcium binding matrix protein of human metapneumovirus.
Authors: Cedric Leyrat / Max Renner / Karl Harlos / Juha T Huiskonen / Jonathan M Grimes /
Abstract: The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus ...The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca²⁺ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca²⁺ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses.
History
DepositionJul 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Sep 20, 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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein M
B: Matrix protein M
C: Matrix protein M
D: Matrix protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8779
Polymers110,6814
Non-polymers1965
Water3,135174
1
A: Matrix protein M
C: Matrix protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4214
Polymers55,3402
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-53 kcal/mol
Surface area21880 Å2
MethodPISA
2
B: Matrix protein M
D: Matrix protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4565
Polymers55,3402
Non-polymers1163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-66 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.009, 62.009, 275.385
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Matrix protein M


Mass: 27670.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Strain: serotype A1 (NL/1/00) / Gene: M / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: Q91F56
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG6000, 100 mM Tris, pH 8.0, 10 mM zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionRedundancy: 9.6 % / Number: 269370 / Rmerge(I) obs: 0.194 / D res high: 2.835 Å / D res low: 275.385 Å / Num. obs: 27947 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRedundancy
2.832.9999.111.8159.9
8.9653.798.810.03510
ReflectionResolution: 2.83→53.701 Å / Num. all: 28144 / Num. obs: 27947 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 76.47 Å2 / Rmerge(I) obs: 0.194 / Rsym value: 0.205 / Net I/σ(I): 9.5
Reflection shellResolution: 2.83→2.99 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.82 / Mean I/σ(I) obs: 1.7 / Rsym value: 1.9 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.77 Å53.7 Å
Translation5.77 Å53.7 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.5.2phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
HKL-2000data reduction
SCALAdata scaling
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQP

2vqp


Resolution: 2.83→53.7 Å / Cor.coef. Fo:Fc: 0.9129 / Cor.coef. Fo:Fc free: 0.8919 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.639 / SU Rfree Blow DPI: 0.314 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1403 5.02 %RANDOM
Rwork0.1851 ---
obs0.1873 27940 99.05 %-
all-28144 --
Displacement parametersBiso max: 289.72 Å2 / Biso mean: 87.8343 Å2 / Biso min: 41.26 Å2
Baniso -1Baniso -2Baniso -3
1--17.5989 Å20 Å20 Å2
2---17.5989 Å20 Å2
3---35.1978 Å2
Refine analyzeLuzzati coordinate error obs: 0.407 Å
Refinement stepCycle: LAST / Resolution: 2.83→53.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6935 0 5 174 7114
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0122399SINUSOIDAL2
X-RAY DIFFRACTIONt_angle_deg1.53150HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion3.48975HARMONIC5
X-RAY DIFFRACTIONt_other_torsion26.37055HARMONIC20
X-RAY DIFFRACTIONt_trig_c_planes0.00853SEMIHARMONIC5
X-RAY DIFFRACTIONt_gen_planes0.01891012SEMIHARMONIC5
X-RAY DIFFRACTIONt_incorr_chiral_ct08146SEMIHARMONIC4
X-RAY DIFFRACTIONt_it07055HARMONIC2
X-RAY DIFFRACTIONt_nbd09585HARMONIC2
LS refinement shellResolution: 2.83→2.94 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2844 141 5.02 %
Rwork0.2265 2665 -
all0.2295 2806 -
obs--99.05 %
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)
10.65781.17770.63281.55390.2990.691-0.03670.0482-0.0098-0.01080.0607-0.0282-0.0469-0.0855-0.024-0.0142-0.10180.00870.025-0.1203-0.00770.03935.4956-37.1518
22.6127-0.09530.3035-0.0714-0.44570.6420.03170.0301-0.0528-0.0398-0.010.0063-0.06630.025-0.0216-0.11110.0998-0.11070.1058-0.0533-0.0143-26.0459-15.434-83.1337
30.34030.5359-0.29811.81550.53740.3917-0.0012-0.0054-0.01330.04850.0141-0.0175-0.0244-0.0683-0.01290.1402-0.0461-0.1223-0.1218-0.0696-0.0145-4.9516-3.895-12.9925
42.21470.34710.18570.2260.35590.61040.0493-0.0575-0.02170.0012-0.0288-0.006-0.088-0.0188-0.0205-0.0819-0.0618-0.1090.08270.0847-0.0042-36.9245-15.6144-58.9145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 254
2X-RAY DIFFRACTION2{ B|* }B1 - 254
3X-RAY DIFFRACTION3{ C|* }C1 - 254
4X-RAY DIFFRACTION4{ D|* }D1 - 254

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