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- PDB-5t1d: Crystal structure of EBV gHgL/gp42/E1D1 complex -

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Basic information

Entry
Database: PDB / ID: 5t1d
TitleCrystal structure of EBV gHgL/gp42/E1D1 complex
Components
  • (Envelope glycoprotein ...) x 2
  • E1D1 IgG2a heavy chain
  • E1D1 IgG2a light chain
  • Glycoprotein 42
KeywordsVIRAL PROTEIN / receptor binding / herpesvirus entry / Epstein-Barr Virus / membrane fusion
Function / homology
Function and homology information


host cell endosome membrane / carbohydrate binding / 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
Viral glycoprotein L / Herpesvirus glycoprotein H, domain D-II / SAND domain / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal ...Viral glycoprotein L / Herpesvirus glycoprotein H, domain D-II / SAND domain / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / 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 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / C-type lectin-like/link domain superfamily / C-type lectin fold / Immunoglobulins / Roll / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Envelope glycoprotein L / Envelope glycoprotein H / Glycoprotein 42
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsSathiyamoorthy, K. / Jardetzky, T.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI119480 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI076183 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA117794 United States
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for Epstein-Barr virus host cell tropism mediated by gp42 and gHgL entry glycoproteins.
Authors: Sathiyamoorthy, K. / Hu, Y.X. / Mohl, B.S. / Chen, J. / Longnecker, R. / Jardetzky, T.S.
History
DepositionAug 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 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
C: Glycoprotein 42
H: E1D1 IgG2a heavy chain
L: E1D1 IgG2a light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,3777
Polymers153,5285
Non-polymers8492
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.510, 166.000, 272.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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

#1: Protein Envelope glycoprotein H / gH


Mass: 72600.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: gH, BXLF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03231
#2: Protein Envelope glycoprotein L / gL


Mass: 12475.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: gL, BKRF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03212

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Antibody , 2 types, 2 molecules HL

#4: Antibody E1D1 IgG2a heavy chain


Mass: 22839.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: E1D1 hybridoma
#5: Antibody E1D1 IgG2a light chain


Mass: 23986.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: E1D1 hybridoma

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Protein / Sugars , 2 types, 3 molecules C

#3: Protein Glycoprotein 42 / gp42


Mass: 21626.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1 / Gene: BZLF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0C6Z5
#6: 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.: 2
Source method: isolated from a genetically manipulated 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

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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: 3.88 Å3/Da / Density % sol: 68.33 %
Description: Slender rod-shaped crystals, initial crystals in PEG 3350 and different citrates resembles the pattern of a cracked tree bark slab
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8.0, 0.18 M Potassium Citrate, 12 % PEG 6000
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.901→46.11 Å / Num. obs: 53195 / % possible obs: 99.83 % / Redundancy: 5.9 % / Biso Wilson estimate: 77.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1232 / Net I/σ(I): 12.21
Reflection shellResolution: 2.901→3.005 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.586 / % possible all: 99.05

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3.1→46.11 Å / SU ML: 0.41 / σ(F): 1.36 / Phase error: 26.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 1977 4.98 %
Rwork0.2116 --
obs0.2143 39681 90.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10554 0 56 0 10610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410893
X-RAY DIFFRACTIONf_angle_d0.63414823
X-RAY DIFFRACTIONf_dihedral_angle_d11.7026460
X-RAY DIFFRACTIONf_chiral_restr0.0421693
X-RAY DIFFRACTIONf_plane_restr0.0041865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17750.3738870.30041776X-RAY DIFFRACTION60
3.1775-3.26340.34051070.29031918X-RAY DIFFRACTION66
3.2634-3.35940.29621110.28742189X-RAY DIFFRACTION74
3.3594-3.46780.3041290.26262361X-RAY DIFFRACTION81
3.4678-3.59170.31611350.24282630X-RAY DIFFRACTION89
3.5917-3.73550.29721470.23692866X-RAY DIFFRACTION97
3.7355-3.90540.26671530.22052959X-RAY DIFFRACTION100
3.9054-4.11120.27391570.20752942X-RAY DIFFRACTION100
4.1112-4.36860.26641540.18522955X-RAY DIFFRACTION100
4.3686-4.70550.18281570.16262966X-RAY DIFFRACTION100
4.7055-5.17850.23181600.16612982X-RAY DIFFRACTION100
5.1785-5.92650.29161550.19123003X-RAY DIFFRACTION100
5.9265-7.46170.2551590.22513025X-RAY DIFFRACTION100
7.4617-46.11480.24351660.20113132X-RAY DIFFRACTION100
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)
13.70761.2941.69544.7356-0.46043.1691-0.0006-0.27530.73720.2458-0.144-0.0584-0.53370.3480.140.2475-0.0973-0.01350.5603-0.28430.8186258.3115219.2246583.7055
22.3553-0.05161.23392.9156-0.70152.4354-0.17920.11030.5802-0.08920.2583-0.164-0.2545-0.14730.03930.2953-0.10420.07560.3066-0.14380.3567232.3644215.557572.1086
33.2835-0.94331.65861.7321-0.76343.22620.13360.27040.2813-0.2170.1644-0.58760.34230.253-0.15760.2186-0.0127-0.01570.2135-0.29780.0517237.8375201.7858572.3379
42.84731.13370.87912.48290.07291.78450.1381-0.14220.316-0.1548-0.00490.00510.11730.0989-0.01120.29710.0234-0.0790.1473-0.0186-0.1101212.3205197.2615562.4824
54.82450.49410.13175.3064-1.37833.83430.3638-0.1548-0.23580.09640.15780.77930.418-0.3707-0.32670.3161-0.0607-0.07990.10880.01450.2831193.2977183.2445561.0652
62.7135-0.22630.30436.3057-1.41524.93680.5779-0.84120.3445-0.24680.05031.2824-0.1634-0.3136-0.48570.3013-0.0579-0.15770.9652-0.57191.0741267.0212222.591592.4005
76.72484.59372.32775.1103-0.43592.88630.0231-0.18550.21830.275-0.44750.1811-0.37460.7170.23750.3756-0.2213-0.06011.0158-0.24981.0308270.5029223.7532582.1274
89.2148-0.22562.64495.5092-3.69781.99990.5239-2.1102-1.87580.30760.55920.88360.6514-1.5813-0.940.5823-0.30550.12231.4523-0.03870.9227276.8099214.8151577.6721
97.6483.01114.02153.98471.2076.5642-0.4175-0.90570.9802-0.08080.10970.2651-0.8313-0.2130.59140.2221-0.14040.01910.8891-0.49120.8157272.6078225.9974590.9327
100.45920.112-0.58247.0902-0.2643.1989-0.1868-0.12720.0864-0.26140.3966-0.06150.0316-0.17680.83630.1836-0.0771-0.0280.4781-0.45120.8408257.5328222.7929581.0439
110.1874-0.6228-0.52354.94644.70994.532-0.56620.45940.573-1.14980.9968-0.2836-0.96710.0154-0.36970.5397-0.0405-0.00070.8136-0.02190.7289259.6979227.9183572.2472
122.4803-2.09420.33851.8374-0.02411.03840.27240.53931.1539-0.19410.186-0.1969-0.07420.0938-0.06030.28390.16990.03821.0970.03620.6053264.0761216.5985573.2057
132.8668-1.06744.00722.4033-2.32635.94340.63651.8275-2.0762-0.4975-0.1459-0.13270.93060.2207-0.54920.44070.1042-0.05721.0442-0.65291.2096270.5066204.9286579.4915
146.74174.67513.78795.9951-1.6798.84980.6198-0.1586-0.7289-0.2440.16390.84150.6813-1.2355-0.68530.3559-0.1297-0.03420.8059-0.08541.2305278.0447210.0165593.4944
153.68080.53613.47442.81411.64665.3146-0.3085-0.89330.6363-0.1645-0.1270.6562-0.7836-0.72990.46410.3024-0.00980.2290.3416-0.06130.3589207.9489212.6684571.1564
160.6651-1.30910.01643.86-1.59251.87580.1109-0.1208-0.41752.2955-0.00230.44820.4428-0.1422-0.04751.0357-0.14910.03150.7035-0.06740.5157229.4309170.5623595.2656
174.48440.37530.30075.59391.82283.7278-0.0701-0.058-0.43811.24670.4902-0.38080.23250.5469-0.33480.84660.0657-0.14040.4818-0.09510.3524233.3295167.2382589.0704
182.8501-1.51740.32072.90120.33590.2033-0.1198-0.87460.18891.12560.2509-0.70.22890.1484-0.06050.71970.0095-0.17180.5715-0.05950.2455235.958175.0878585.476
193.50110.22960.8012.14750.19020.7016-0.1634-1.31910.6750.2354-0.60520.8777-0.2028-0.10720.63140.2552-0.13940.08011.0505-0.39110.7662288.5635228.6863605.6009
204.32070.0195-1.32252.57090.03270.4060.9451-2.4236-1.02960.6034-0.37420.27990.5306-0.019-0.4680.5283-0.3566-0.00031.4478-0.00040.8513288.6735218.5605607.9869
215.1490.0082-2.5325.37462.98635.81550.4282-3.0240.5471-0.0831-0.4538-0.10540.09090.14130.07330.7279-0.2950.04581.6689-0.33920.5264285.6024223.8409613.2476
221.15490.28921.1490.89870.67571.29910.4447-1.1608-0.37830.5363-0.48140.00340.4278-1.21260.04740.532-0.20520.0850.9479-0.08240.3465300.6995228.2179610.5204
238.5431.66657.7568.43192.06157.0793-0.09160.7794-1.6756-0.52040.3945-3.3183-0.0121.984-0.00030.6374-0.14740.28280.4451-0.04331.5394340.3105231.5569603.5729
245.9422-2.05040.15534.6331.54942.04640.19980.23070.3589-0.16330.0209-0.8045-0.4618-0.414-0.18650.39310.14320.09960.0346-0.06750.4239320.6474234.8231606.8908
257.4104-0.5486-0.99551.77063.23265.87760.1902-0.53740.7761-0.46430.2166-0.8323-1.04590.9127-0.41560.4537-0.05650.13730.29650.01990.8682328.6977242.2564604.5167
263.2617-0.86781.8251.11190.51853.34850.9516-0.3399-1.05780.01020.36810.27110.9327-0.0815-0.05510.3264-0.1187-0.34330.3479-0.05540.7965305.863209.8574592.1773
276.7835-4.5431-4.92856.252-0.68718.5411.36590.6507-3.49270.2713-0.64160.77650.9356-1.5264-0.84940.5472-0.1082-0.15110.90760.21371.1227288.4805202.5452596.3608
281.69630.39031.09993.17493.16564.33640.3688-0.0616-0.2161-0.5541-0.23170.4745-0.0652-0.52820.06480.1253-0.1494-0.12130.32-0.29710.3417297.3363219.4331593.6838
291.5146-0.6048-0.38071.70240.44450.53240.3849-0.2684-0.75650.0246-0.22970.1190.3617-0.1887-0.20350.3541-0.1348-0.00220.28050.01280.7923294.3396211.5402586.4319
304.37960.44952.02564.17460.01414.84380.5897-0.5993-0.81550.07940.18810.35211.2004-1.2294-0.21830.1885-0.2305-0.20460.5918-0.04920.521298.1661214.2756594.2927
311.91320.24610.15261.308-0.93552.7633-0.2173-0.42230.05110.14530.1869-0.1758-0.2859-0.02440.02730.12190.0652-0.12870.3089-0.31580.5564325.7742225.3611603.5974
326.8355-0.5023.37994.0784-0.10645.87570.0362-0.8124-1.39630.97020.6022-0.04440.4794-0.4119-0.59960.2990.0387-0.05470.2637-0.04410.5731328.4453219.041607.0896
335.5042-1.23083.16134.8984-2.33916.87650.7969-0.54090.10760.06840.29650.8033-0.2065-0.3701-0.96250.2786-0.00720.17340.1515-0.1180.7405320.0654222.9753601.365
344.2306-1.271-2.87334.96562.20262.3542-0.1519-1.086-0.47651.21690.6528-0.38040.55990.9674-0.53760.53970.2883-0.13410.3177-0.01710.7642333.8668221.1168611.9672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 514 )
5X-RAY DIFFRACTION5chain 'A' and (resid 515 through 674 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 47 )
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 52 )
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 102 )
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 111 )
12X-RAY DIFFRACTION12chain 'B' and (resid 112 through 117 )
13X-RAY DIFFRACTION13chain 'B' and (resid 118 through 127 )
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 135 )
15X-RAY DIFFRACTION15chain 'C' and (resid 43 through 79 )
16X-RAY DIFFRACTION16chain 'C' and (resid 80 through 109 )
17X-RAY DIFFRACTION17chain 'C' and (resid 110 through 183 )
18X-RAY DIFFRACTION18chain 'C' and (resid 184 through 219 )
19X-RAY DIFFRACTION19chain 'H' and (resid 1 through 39 )
20X-RAY DIFFRACTION20chain 'H' and (resid 40 through 59 )
21X-RAY DIFFRACTION21chain 'H' and (resid 60 through 83 )
22X-RAY DIFFRACTION22chain 'H' and (resid 84 through 125 )
23X-RAY DIFFRACTION23chain 'H' and (resid 126 through 136 )
24X-RAY DIFFRACTION24chain 'H' and (resid 137 through 182 )
25X-RAY DIFFRACTION25chain 'H' and (resid 183 through 213 )
26X-RAY DIFFRACTION26chain 'L' and (resid 1 through 22 )
27X-RAY DIFFRACTION27chain 'L' and (resid 23 through 37 )
28X-RAY DIFFRACTION28chain 'L' and (resid 38 through 53 )
29X-RAY DIFFRACTION29chain 'L' and (resid 54 through 80 )
30X-RAY DIFFRACTION30chain 'L' and (resid 81 through 105 )
31X-RAY DIFFRACTION31chain 'L' and (resid 106 through 134 )
32X-RAY DIFFRACTION32chain 'L' and (resid 135 through 160 )
33X-RAY DIFFRACTION33chain 'L' and (resid 161 through 178 )
34X-RAY DIFFRACTION34chain 'L' and (resid 179 through 217 )

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