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- PDB-2xqy: CRYSTAL STRUCTURE OF PSEUDORABIES CORE FRAGMENT OF GLYCOPROTEIN H... -

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Basic information

Entry
Database: PDB / ID: 2xqy
TitleCRYSTAL STRUCTURE OF PSEUDORABIES CORE FRAGMENT OF GLYCOPROTEIN H IN COMPLEX WITH FAB D6.3
Components
  • (A13-D6.3 MONOCLONAL ...) x 2
  • ENVELOPE GLYCOPROTEIN H
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / ENVELOPE PROTEIN
Function / homology
Function and homology information


host cell endosome membrane / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1340 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 - #50 / Herpesvirus glycoprotein H, C-terminal domain / 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 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1340 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 - #50 / Herpesvirus glycoprotein H, C-terminal domain / 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 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Envelope glycoprotein H
Similarity search - Component
Biological speciesSUID HERPESVIRUS
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBackovic, M. / Dubois, R. / Cockburn, J. / Sharff, A. / Vaney, M. / Granzow, H. / Klupp, B. / Bricogne, G. / Mettenleiter, T. / Rey, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of a Core Fragment of Glycoprotein H from Pseudorabies Virus in Complex with Antibody.
Authors: Backovic, M. / Dubois, R.M. / Cockburn, J.J. / Sharff, A.J. / Vaney, M.C. / Granzow, H. / Klupp, B.G. / Bricogne, G. / Mettenleiter, T.C. / Rey, F.A.
History
DepositionSep 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / software / struct_asym / struct_conn / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _software.name / _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 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
E: ENVELOPE GLYCOPROTEIN H
G: A13-D6.3 MONOCLONAL ANTIBODY
J: A13-D6.3 MONOCLONAL ANTIBODY
K: A13-D6.3 MONOCLONAL ANTIBODY
L: A13-D6.3 MONOCLONAL ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,87912
Polymers225,5366
Non-polymers2,3436
Water17,150952
1
A: ENVELOPE GLYCOPROTEIN H
G: A13-D6.3 MONOCLONAL ANTIBODY
L: A13-D6.3 MONOCLONAL ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0416
Polymers112,7683
Non-polymers1,2733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: ENVELOPE GLYCOPROTEIN H
J: A13-D6.3 MONOCLONAL ANTIBODY
K: A13-D6.3 MONOCLONAL ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8386
Polymers112,7683
Non-polymers1,0703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.310, 100.630, 161.830
Angle α, β, γ (deg.)90.00, 94.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9998, 0.0205, -0.0048), (-0.0207, 0.9994, -0.0286), (0.0042, 0.0287, 0.9996)10.385, 47.697, -1.951
2given(0.997, 0.0774, 0.0013), (-0.0773, 0.9969, -0.0144), (-0.0024, 0.0142, 0.9999)9.594, 46.769, -2.052
3given(0.9961, -0.0887, -0.0017), (0.0887, 0.996, -0.0046), (0.0021, 0.0045, 1)-5.337, -47.699, 1.579

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Components

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Antibody , 2 types, 4 molecules GJKL

#2: Antibody A13-D6.3 MONOCLONAL ANTIBODY


Mass: 28098.064 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN OF FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell: B CELL HYBRIDOMA / Cell line: A13-D6.3 MURINE B CELL HYBRIDOMA / Plasmid: PMT-FAB-STREP / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly)
#3: Antibody A13-D6.3 MONOCLONAL ANTIBODY


Mass: 24278.783 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN OF FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell: B CELL HYBRIDOMA / Cell line: A13-D6.3 MURINE B CELL HYBRIDOMA / Plasmid: PMT-FAB-STREP / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly)

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Protein / Non-polymers , 2 types, 954 molecules AE

#1: Protein ENVELOPE GLYCOPROTEIN H / GH


Mass: 60391.078 Da / Num. of mol.: 2 / Fragment: RESIDUES 107-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUID HERPESVIRUS / Strain: 1 / Plasmid: PT350 / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P27416
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 952 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 6 molecules

#4: 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.: 5
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
#5: 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.: 1
Source method: isolated from a genetically manipulated 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

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Details

Sequence detailsPHE610 IS MODELED WITHOUT SIDE CHAIN. THE SEQUENCE DEPOSITED UNDER GB CBI70317.1 (CHAINS G AND J) ...PHE610 IS MODELED WITHOUT SIDE CHAIN. THE SEQUENCE DEPOSITED UNDER GB CBI70317.1 (CHAINS G AND J) CONTAINS THE WHOLE HEAVY CHAIN OF THE MONOCLONAL ANTIBODY THAT THE FAB D6.3 FRAGMENT IS DERIVED FROM. THE SEQUENCE COPIED HERE CORRESPONDS TO THE HEAVY CHAIN FRAGMENT THAT CONTRIBUTES TO THE FAB, I.E. IT DOES NOT CONTAIN THE FC C-TERMINAL REGION. CHAINS K AND L ARE GB CBI70318.1. THE CHAINS A AND E HAS C-TERMINAL DOUBLE STREP-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: 3.45 Å3/Da / Density % sol: 57.4 % / Description: NONE
Crystal growpH: 8
Details: 0.1M IMIDAZOLE PH 8, 0.7M SODIUM FORMATE, 10.5% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.1399
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1399 Å / Relative weight: 1
ReflectionResolution: 2.05→58.13 Å / Num. obs: 151575 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 52.49 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.3
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.3 / % possible all: 55.3

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Processing

Software
NameVersionClassification
BUSTER2.11.0refinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BBD

1bbd


Resolution: 2.05→58.12 Å / Cor.coef. Fo:Fc: 0.9521 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 7603 5.02 %RANDOM
Rwork0.1878 ---
obs0.1887 151525 91.85 %-
Displacement parametersBiso mean: 70.46 Å2
Baniso -1Baniso -2Baniso -3
1--5.8034 Å20 Å29.3841 Å2
2---0.465 Å20 Å2
3---6.2684 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: LAST / Resolution: 2.05→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13625 0 154 952 14731
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114122HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0219265HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4594SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes288HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2218HARMONIC5
X-RAY DIFFRACTIONt_it14122HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.43
X-RAY DIFFRACTIONt_other_torsion17.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1899SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15695SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2859 258 5.02 %
Rwork0.2483 4878 -
all0.2501 5136 -
obs--91.85 %
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)
11.7111-0.3663-0.7450.38110.37152.28880.01090.2990.1843-0.0198-0.0319-0.0499-0.0306-0.41860.021-0.1650.0128-0.09280.00560.0527-0.22-29.588315.4618-59.3063
21.6298-0.3198-0.860.54530.57531.91840.00980.30510.1004-0.0074-0.024-0.03450.0741-0.24230.0142-0.10610.001-0.0963-0.0259-0.0343-0.2161-18.446465.4495-60.9675
31.2129-0.45720.55641.2845-0.34291.8033-0.11140.10950.24630.1126-0.0485-0.1218-0.31970.01930.15980.1144-0.0467-0.0746-0.25240.0301-0.1145-12.587823.6448-23.3323
41.3596-0.51570.670.8405-0.26091.6621-0.11490.16750.1653-0.0532-0.0325-0.1227-0.03090.26910.14750.0786-0.0329-0.0365-0.17110.0154-0.1048-1.158271.6415-25.0165
52.1241-0.40041.32790.927-0.38781.78290.1694-0.0035-0.16160.0221-0.054-0.05850.24840.1529-0.11530.0781-0.0455-0.0489-0.22490.0057-0.1229-0.997555.7525-16.0628
61.949-0.19661.08150.9174-0.15371.8074-0.01420.02130.14140.16210.0069-0.0365-0.0104-0.01440.00720.0382-0.0209-0.0554-0.2116-0.0121-0.1039-11.41417.7452-14.343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN E)
3X-RAY DIFFRACTION3(CHAIN G)
4X-RAY DIFFRACTION4(CHAIN J)
5X-RAY DIFFRACTION5(CHAIN K)
6X-RAY DIFFRACTION6(CHAIN L)

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