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- PDB-4c3d: HRSV M2-1, P422 crystal form -

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Basic information

Entry
Database: PDB / ID: 4c3d
TitleHRSV M2-1, P422 crystal form
ComponentsMATRIX M2-1
KeywordsVIRAL PROTEIN / M2-1 PROTEIN
Function / homology
Function and homology information


: / regulation of viral transcription / viral transcription / transcription antitermination / virion component / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Pneumovirus matrix protein 2 (M2), zinc-binding domain / Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / 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 RESPIRATORY SYNCYTIAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsTanner, S.J. / Ariza, A. / Richard, C.A. / Wu, W. / Trincao, J. / Hiscox, J.A. / Carroll, M.W. / Silman, N.J. / Eleouet, J.F. / Edwards, T.A. / Barr, J.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal Structure of the Essential Transcription Antiterminator M2-1 Protein of Human Respiratory Syncytial Virus and Implications of its Phosphorylation.
Authors: Tanner, S.J. / Ariza, A. / Richard, C. / Kyle, H.F. / Dods, R.L. / Blondot, M. / Wu, W. / Trincao, J. / Trinh, C.H. / Hiscox, J.A. / Carroll, M.W. / Silman, N.J. / Eleouet, J. / Edwards, T.A. / Barr, J.N.
History
DepositionAug 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: MATRIX M2-1
B: MATRIX M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6536
Polymers45,2042
Non-polymers4504
Water1,08160
1
A: MATRIX M2-1
hetero molecules

A: MATRIX M2-1
hetero molecules

A: MATRIX M2-1
hetero molecules

A: MATRIX M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,30612
Polymers90,4074
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area13870 Å2
ΔGint-81 kcal/mol
Surface area34840 Å2
MethodPISA
2
B: MATRIX M2-1
hetero molecules

B: MATRIX M2-1
hetero molecules

B: MATRIX M2-1
hetero molecules

B: MATRIX M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,30612
Polymers90,4074
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14030 Å2
ΔGint-80 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.275, 102.275, 90.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21A-2017-

HOH

31A-2040-

HOH

41B-2005-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 4 - 173 / Label seq-ID: 9 - 178

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein MATRIX M2-1 / HRSV M2-1 / ENVELOPE-ASSOCIATED 22 KDA PROTEIN


Mass: 22601.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS / Strain: A2 / Plasmid: PGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P04545
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE INITIAL AMINO ACIDS ARE THE REMNANTS OF REMOVING AN N- TERMINAL GST TAG

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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: 6.64 Å3/Da / Density % sol: 80 % / Description: NONE
Crystal growpH: 10 / Details: 30 % (V/V) PEG 400, 0.01 M CDCL2, 0.1 M CAPS PH 10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2823
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2823 Å / Relative weight: 1
ReflectionResolution: 2.52→45.74 Å / Num. obs: 16695 / % possible obs: 98.9 % / Redundancy: 30 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.8
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.8 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.52→45.74 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.591 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26323 845 5.1 %RANDOM
Rwork0.21095 ---
obs0.21351 15849 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.325 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.52→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 4 60 2668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192644
X-RAY DIFFRACTIONr_bond_other_d0.0040.022644
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9643554
X-RAY DIFFRACTIONr_angle_other_deg0.9436077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00823.984123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21615527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3721521
X-RAY DIFFRACTIONr_chiral_restr0.0790.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022918
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02607
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0276.8931280
X-RAY DIFFRACTIONr_mcbond_other6.0216.891279
X-RAY DIFFRACTIONr_mcangle_it8.45410.3111593
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.3247.481360
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9563 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 51 -
Rwork0.222 1048 -
obs--88.77 %

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