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- PDB-3m1c: Crystal structure of the conserved herpesvirus fusion regulator c... -

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Basic information

Entry
Database: PDB / ID: 3m1c
TitleCrystal structure of the conserved herpesvirus fusion regulator complex gH-gL
Components(Envelope glycoprotein ...) x 2
KeywordsVIRAL PROTEIN / glycoprotein H / glycoprotein L / gH/gL / envelope protein / Herpes simplex virus / Disulfide bond / Glycoprotein / Host cell membrane / Host endosome / Host membrane / Membrane / Transmembrane / Virion / Virus reference strain
Function / homology
Function and homology information


host cell endosome membrane / host cell Golgi apparatus / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Antimicrobial Peptide, Beta-defensin 2; Chain A - #40 / Enolase-like; domain 1 - #170 / Herpesvirus glycoprotein L, C-terminal / dsDNA virus glycoprotein L C terminal / Herpesvirus glycoprotein L, N-terminal / Herpesvirus glycoprotein L, N-terminal domain superfamily / Herpesvirus glycoprotein L / Alphaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein H, C-terminal domain / Antimicrobial Peptide, Beta-defensin 2; Chain A ...Antimicrobial Peptide, Beta-defensin 2; Chain A - #40 / Enolase-like; domain 1 - #170 / Herpesvirus glycoprotein L, C-terminal / dsDNA virus glycoprotein L C terminal / Herpesvirus glycoprotein L, N-terminal / Herpesvirus glycoprotein L, N-terminal domain superfamily / Herpesvirus glycoprotein L / Alphaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein H, C-terminal domain / Antimicrobial Peptide, Beta-defensin 2; Chain A / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Enolase-like; domain 1 / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Xylitol / Envelope glycoprotein L / Envelope glycoprotein H
Similarity search - Component
Biological speciesHuman herpesvirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsChowdary, T.K. / Heldwein, E.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Crystal structure of the conserved herpesvirus fusion regulator complex gH-gL.
Authors: Chowdary, T.K. / Cairns, T.M. / Atanasiu, D. / Cohen, G.H. / Eisenberg, R.J. / Heldwein, E.E.
History
DepositionMar 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8356
Polymers104,8162
Non-polymers1,0194
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-38 kcal/mol
Surface area38440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.255, 88.255, 333.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein H / gH


Mass: 81626.977 Da / Num. of mol.: 1
Fragment: extracellular domain of glycoprotein H, residues 48-803
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Species: Human simplex virus 2 / Strain: HG52 / Gene: Envelope glycoprotein H, gH, UL22 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P89445
#2: Protein Envelope glycoprotein L / gL


Mass: 23189.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Species: Human simplex virus 2 / Strain: HG52 / Gene: Envelope glycoprotein L, gL, UL1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P28278

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Sugars , 3 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H12O5

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Non-polymers , 1 types, 52 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 298 K
Details: 20% PEG 4000, 0.1M Sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2009
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionRedundancy: 16.3 % / Av σ(I) over netI: 10.79 / Number: 343790 / Rmerge(I) obs: 0.188 / Χ2: 1.29 / D res high: 3.3 Å / D res low: 40 Å / Num. obs: 21100 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.934010010.0643.10214
7.18.9310010.0821.86315
6.27.110010.1221.46415.7
5.646.210010.1321.21916
5.245.6410010.1381.21916.3
4.935.2410010.1231.16516.3
4.684.9310010.1281.20116.3
4.484.6810010.1411.16316.6
4.314.4810010.1541.16916.5
4.164.3110010.1811.16416.6
4.034.1610010.2141.1316.7
3.914.0310010.2411.12716.7
3.813.9110010.2651.1516.7
3.723.8110010.2961.1616.9
3.633.7210010.3521.10716.7
3.553.6310010.3891.07916.9
3.483.5510010.4241.08316.8
3.423.4810010.4881.05716.8
3.363.4210010.5991.07716.4
3.33.3610010.6481.15616.4
ReflectionResolution: 2.84→50 Å / Num. obs: 32326 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.6
Reflection shellResolution: 2.84→2.89 Å / Redundancy: 5.9 % / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
PHENIX1.4_175refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→39.2 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / Isotropic thermal model: TLS / σ(F): 0.2 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 2475 9.52 %
Rwork0.17 --
obs0.176 25991 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.21 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 59.18 Å2
Baniso -1Baniso -2Baniso -3
1-5.837 Å20 Å2-0 Å2
2--5.837 Å2-0 Å2
3----11.673 Å2
Refinement stepCycle: LAST / Resolution: 3→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 66 52 6708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096829
X-RAY DIFFRACTIONf_angle_d1.2159318
X-RAY DIFFRACTIONf_dihedral_angle_d18.8132438
X-RAY DIFFRACTIONf_chiral_restr0.0761062
X-RAY DIFFRACTIONf_plane_restr0.0051215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05780.33631270.23981102X-RAY DIFFRACTION82
3.0578-3.12020.35061200.24351187X-RAY DIFFRACTION88
3.1202-3.1880.31641390.20741151X-RAY DIFFRACTION87
3.188-3.26210.29481230.19331249X-RAY DIFFRACTION91
3.2621-3.34360.23021280.1771248X-RAY DIFFRACTION92
3.3436-3.4340.29121260.17921270X-RAY DIFFRACTION94
3.434-3.5350.26481300.17551297X-RAY DIFFRACTION94
3.535-3.6490.23651390.16561289X-RAY DIFFRACTION96
3.649-3.77930.2371420.16051302X-RAY DIFFRACTION97
3.7793-3.93050.21141350.1471322X-RAY DIFFRACTION96
3.9305-4.10920.27491420.14911320X-RAY DIFFRACTION97
4.1092-4.32560.2071390.13351330X-RAY DIFFRACTION97
4.3256-4.59620.21071410.13231373X-RAY DIFFRACTION98
4.5962-4.95050.19521440.12521365X-RAY DIFFRACTION98
4.9505-5.44750.21841460.13781363X-RAY DIFFRACTION98
5.4475-6.2330.20731490.14771394X-RAY DIFFRACTION98
6.233-7.84260.22561440.15151424X-RAY DIFFRACTION98
7.8426-39.19850.19171610.17721530X-RAY DIFFRACTION99
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)
10.6428-0.2938-0.76171.02631.18853.40380.0349-0.00570.1703-0.13460.2166-0.2971-0.77690.4335-00.3971-0.0104-0.00790.2577-0.05380.330428.932662.9562139.5017
21.13360.724-0.1672.67130.79451.9075-0.048-0.03560.0945-0.26410.1929-0.0635-0.21670.1884-0.00010.08790.01250.01350.2388-0.05990.253331.620438.344114.5897
33.25050.46570.50873.81590.62151.36250.09320.132-0.4528-0.1675-0.09910.06310.22070.01310.00050.08210.06610.02020.2454-0.070.232423.264810.0059112.2203
40.30580.32140.04540.3697-0.06920.3235-0.1826-0.0598-0.76640.677-0.11040.43060.3906-0.3443-0.00120.42220.05130.10010.5731-0.07290.49289.781258.0508155.9645
51.7977-0.6741-0.40961.68490.74571.8627-0.08220.0891-0.052-0.26280.1718-0.0908-0.47150.0765-0.00020.38680.12550.02780.1814-0.05420.124321.679963.4953150.7866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 49:303)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 304:614)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 615:797)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 24:51)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 52:165)

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