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

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Basic information

Entry
Database: PDB / ID: 4csa
TitleCrystal structure of the asymmetric human metapneumovirus M2-1 tetramer bound to a DNA 4-mer
Components
  • (M2-1) x 2
  • 5'-D(*AP*GP*TP*TP*AP)-3'
KeywordsVIRAL PROTEIN/DNA / VIRAL PROTEIN-DNA COMPLEX / 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: 2.28 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 1.3Dec 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
G: 5'-D(*AP*GP*TP*TP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,61110
Polymers87,2575
Non-polymers3545
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15850 Å2
ΔGint-43.5 kcal/mol
Surface area30400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.140, 93.900, 85.510
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABEC

#1: Protein M2-1


Mass: 21434.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
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

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DNA chain , 1 types, 1 molecules G

#3: DNA chain 5'-D(*AP*GP*TP*TP*AP)-3'


Mass: 1519.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN METAPNEUMOVIRUS

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Non-polymers , 3 types, 207 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.3 Å3/Da / Density % sol: 48.5 % / 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: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→63.04 Å / Num. obs: 35938 / % possible obs: 99.7 % / Observed criterion σ(I): 1.8 / Redundancy: 6.5 % / Biso Wilson estimate: 58.74 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.6
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.8 / % possible all: 98.8

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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 4CS8

4cs8


Resolution: 2.28→31.67 Å / Cor.coef. Fo:Fc: 0.9459 / Cor.coef. Fo:Fc free: 0.9364 / SU R Cruickshank DPI: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.271 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1792 4.99 %RANDOM
Rwork0.1935 ---
obs0.195 35900 99.66 %-
Displacement parametersBiso mean: 74.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.4509 Å20 Å214.9087 Å2
2---2.0185 Å20 Å2
3---3.4695 Å2
Refine analyzeLuzzati coordinate error obs: 0.342 Å
Refinement stepCycle: LAST / Resolution: 2.28→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5229 80 10 202 5521
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095400HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037276HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1997SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes756HARMONIC5
X-RAY DIFFRACTIONt_it5400HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion23.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion686SEMIHARMONIC5
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_contact6182SEMIHARMONIC4
LS refinement shellResolution: 2.28→2.35 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2315 127 4.4 %
Rwork0.2326 2758 -
all0.2326 2885 -
obs--99.66 %
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)
10.31160.1928-0.31670.544-0.47760.4271-0.0027-0.01170.0099-0.01190.0167-0.0310.0515-0.0245-0.0141-0.0178-0.0539-0.0134-0.00370.005-0.0197125.6517-14.6948266.5193
20.6391-0.37050.37440-0.30650.91430.0124-0.03830.0343-0.02310.00960.0078-0.0077-0.0219-0.0220.089-0.0679-0.0095-0.04550.0248-0.0609145.714-13.455303.4813
30.0193-0.3285-0.13720.4071-0.10141.2932-0.01530.08-0.03360.10210.0158-0.0641-0.02660.0226-0.0006-0.1014-0.0556-0.00030.031-0.08010.0359142.1915-3.2741262.4013
40.939-0.25210.76450.1034-0.681.00170.01450.0613-0.06140.0651-0.0112-0.04350.0116-0.0674-0.00330.0379-0.0381-0.0795-0.03930.0066-0.0259129.4771-14.5062286.4329
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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