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- PDB-4cs9: Crystal structure of the asymmetric human metapneumovirus M2-1 te... -

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Basic information

Entry
Database: PDB / ID: 4cs9
TitleCrystal structure of the asymmetric human metapneumovirus M2-1 tetramer bound to adenosine monophosphate
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 / virion component / host cell cytoplasm / nucleotide binding / host cell nucleus / structural molecule activity / zinc ion binding
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
ADENOSINE MONOPHOSPHATE / Protein M2-1
Similarity search - Component
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,38912
Polymers85,7384
Non-polymers1,6518
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15350 Å2
ΔGint-61.5 kcal/mol
Surface area31840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.050, 93.610, 85.600
Angle α, β, γ (deg.)90.00, 95.76, 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
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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.33 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: 2.01→49.8 Å / Num. obs: 51659 / % possible obs: 98.8 % / Observed criterion σ(I): 1.8 / Redundancy: 12.8 % / Biso Wilson estimate: 42.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.5
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.8 / % possible all: 85.1

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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: 2.01→49.8 Å / Cor.coef. Fo:Fc: 0.9538 / Cor.coef. Fo:Fc free: 0.9425 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.14
Details: THE RIBOSE AND PHOSPHATE OF AMP4 WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 2626 5.09 %RANDOM
Rwork0.1864 ---
obs0.1875 51637 98.79 %-
Displacement parametersBiso mean: 53.74 Å2
Baniso -1Baniso -2Baniso -3
1-2.2178 Å20 Å27.6182 Å2
2---2.6941 Å20 Å2
3---0.4763 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.01→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5258 0 96 438 5792
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015435HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.967326HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2023SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes816HARMONIC5
X-RAY DIFFRACTIONt_it5435HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion20.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion696SEMIHARMONIC5
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_contact6520SEMIHARMONIC4
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2731 176 5.42 %
Rwork0.2435 3071 -
all0.2452 3247 -
obs--98.79 %
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)
10.05420.1771-0.04180.3222-0.30120.59260.0048-0.0091-0.0044-0.02010.0122-0.01340.03570.0018-0.017-0.0165-0.0287-0.00050.00390.0232-0.023984.41080.0022181.8558
20.4203-0.25820.32540-0.3010.64060.0057-0.03860.0292-0.02340.01010.0113-0.0055-0.004-0.01580.0536-0.0422-0.0008-0.03080.0129-0.0292104.60491.3463218.9408
30.0063-0.1779-0.0810.32110.03020.9861-0.00760.0779-0.01090.08120.0035-0.0388-0.030.01740.0041-0.0703-0.0605-0.00440.0485-0.0390.0007101.155311.174177.841
40.5438-0.01880.46380.1183-0.49270.77350.01750.0458-0.05060.049-0.0202-0.02670.0005-0.04620.00270.0231-0.0431-0.0606-0.02850.0177-0.023188.16460.3464201.6364
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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