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- PDB-4cs7: Crystal structure of the asymmetric human metapneumovirus M2-1 te... -

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Basic information

Entry
Database: PDB / ID: 4cs7
TitleCrystal structure of the asymmetric human metapneumovirus M2-1 tetramer, form 1
ComponentsM2-1
KeywordsVIRAL PROTEIN / ANTITERMINATOR / TRANSCRIPTION ELONGATION / RNA-BINDING / MODULAR PROTEIN / ASYMMETRIC TETRAMER
Function / homology
Function and homology information


regulation of viral transcription / translation elongation factor activity / virion component / host cell cytoplasm / nucleotide binding / host cell nucleus / structural molecule activity / metal ion binding / cytoplasm
Similarity search - Function
Pneumovirus matrix protein 2 (M2), zinc-binding domain / Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.47 Å
AuthorsLeyrat, C. / Renner, M. / Harlos, K. / Grimes, J.M.
CitationJournal: Elife / Year: 2014
Title: Drastic Changes in Conformational Dynamics of the Antiterminator M2-1 Regulate Transcription Efficiency in Pneumovirinae.
Authors: Leyrat, C. / Renner, M. / Harlos, K. / Huiskonen, J.T. / Grimes, J.M.
History
DepositionMar 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_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: M2-1
B: M2-1
C: M2-1
E: M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9998
Polymers85,7374
Non-polymers2624
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13470 Å2
ΔGint-41.3 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.150, 92.670, 82.830
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
M2-1


Mass: 21434.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ZN ION COORDINATED BY C7, C15, C21 AND H25 / Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Strain: NL1-00 (A1) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q8QN58
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.24 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 6.5
Details: 28 % W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, 0.100 M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2828, 1.2802
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28281
21.28021
ReflectionResolution: 2.47→33.13 Å / Num. obs: 27190 / % possible obs: 99.8 % / Observed criterion σ(I): 1.7 / Redundancy: 6.7 % / Biso Wilson estimate: 73.86 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.47→33.13 Å / Cor.coef. Fo:Fc: 0.9359 / Cor.coef. Fo:Fc free: 0.9222 / SU R Cruickshank DPI: 0.58 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.528 / SU Rfree Blow DPI: 0.279 / SU Rfree Cruickshank DPI: 0.289
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5443. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5443. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4.
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1362 5.02 %RANDOM
Rwork0.2334 ---
obs0.2348 27158 99.78 %-
Displacement parametersBiso mean: 102.03 Å2
Baniso -1Baniso -2Baniso -3
1--7.0012 Å20 Å20.4124 Å2
2--8.1079 Å20 Å2
3----1.1067 Å2
Refine analyzeLuzzati coordinate error obs: 0.587 Å
Refinement stepCycle: LAST / Resolution: 2.47→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5365 0 4 78 5447
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125445HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.187330HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2020SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes778HARMONIC5
X-RAY DIFFRACTIONt_it5445HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion18.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion699SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance16HARMONIC1
X-RAY DIFFRACTIONt_utility_angle16HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6291SEMIHARMONIC4
LS refinement shellResolution: 2.47→2.56 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2932 131 4.58 %
Rwork0.2445 2731 -
all0.2469 2862 -
obs--99.78 %
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)
11.90450.14240.08356.54191.07833.5848-0.08040.0863-0.1253-0.2214-0.00930.83470.4336-0.02890.08980.31040.0205-0.12020.48530.0040.341316.35744.08170.938
23.3790.27283.707700.50812.92670.1908-0.21790.17410.2574-0.13830.00610.2613-0.185-0.05241.1515-0.0967-0.24520.4856-0.00960.4345-5.58647.21935.59
30.05620.675-0.45242.1237-0.29192.3903-0.08380.18360.0306-0.515-0.08210.6749-0.1078-0.55010.16590.28010.1435-0.16950.7039-0.05130.9226-0.37356.07175.346
40.16310.21980.21781.12672.31735.99950.05570.1703-0.0607-0.6616-0.05970.22920.1119-0.30550.00390.82940.0295-0.22780.5392-0.02040.336713.40245.01950.497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|169 }
2X-RAY DIFFRACTION2{ B|4 - B|169 }
3X-RAY DIFFRACTION3{ C|3 - C|174 }
4X-RAY DIFFRACTION4{ E|2 - E|169 }

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