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- PDB-4cs8: Crystal structure of the asymmetric human metapneumovirus M2-1 te... -

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Basic information

Entry
Database: PDB / ID: 4cs8
TitleCrystal structure of the asymmetric human metapneumovirus M2-1 tetramer, form 2
Components(M2-1) x 2
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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)86,0008
Polymers85,7384
Non-polymers2624
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14770 Å2
ΔGint-40.2 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.980, 93.420, 85.210
Angle α, β, γ (deg.)90.00, 95.44, 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.: 3
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: Protein M2-1


Mass: 21435.250 Da / Num. of mol.: 1
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
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 48.3 % / 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: I24 / Wavelength: 0.96862
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.1→44.81 Å / Num. obs: 45494 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Biso Wilson estimate: 46.46 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CS7

4cs7


Resolution: 2.1→30.75 Å / Cor.coef. Fo:Fc: 0.9492 / Cor.coef. Fo:Fc free: 0.9434 / SU R Cruickshank DPI: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.162
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2292 5.04 %RANDOM
Rwork0.1923 ---
obs0.1938 45458 99.85 %-
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.0432 Å20 Å29.9413 Å2
2---2.4508 Å20 Å2
3---2.494 Å2
Refine analyzeLuzzati coordinate error obs: 0.295 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5218 0 4 314 5536
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095295HARMONIC2
X-RAY DIFFRACTIONt_angle_deg17122HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1969SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes749HARMONIC5
X-RAY DIFFRACTIONt_it5295HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion22.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion676SEMIHARMONIC5
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_contact6338SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2244 179 5.38 %
Rwork0.2297 3151 -
all0.2294 3330 -
obs--99.85 %
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)
10.31920.1894-0.2030.583-0.28860.394-0.0027-0.02190.00160.00320.0199-0.0360.0522-0.0131-0.0172-0.0342-0.0659-0.00790.00380.02-0.0072134.91220.3537181.0425
20.7435-0.37020.60960-0.36731.17040.0069-0.04220.0451-0.04210.0225-0.00120.0137-0.0126-0.02940.0775-0.057-0.0024-0.03450.0186-0.0714155.40671.5164217.7378
30.0199-0.3277-0.15120.3993-0.08580.985-0.00340.0628-0.0410.0906-0.0022-0.0841-0.03710.03450.0056-0.0947-0.06540.00260.0262-0.04970.0391151.491311.4778176.7771
40.5885-0.15570.44310.0623-0.72691.11280.01860.0532-0.06420.0733-0.025-0.04110.0044-0.06660.00630.0244-0.0697-0.0792-0.0208-0.002-0.0093139.05870.3982201.0015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN E

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