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- PDB-4l1r: Glycoprotein B from Herpes Simplex Virus type 1, A549T Rate-of-En... -

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Basic information

Entry
Database: PDB / ID: 4l1r
TitleGlycoprotein B from Herpes Simplex Virus type 1, A549T Rate-of-Entry mutant, low-pH
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / Coiled-Coil / envelope glycoprotein / membrane fusion / rate of entry / entry rate / Pleckstrin homology domain / Viral Entry / Heparan sulfate
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3280 / SH3 type barrels. - #1230 / PH-domain like - #100 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / PH-domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.0255 Å
AuthorsStampfer, S.D. / Heldwein, E.E.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)160,01811
Polymers157,8072
Non-polymers2,2129
Water55831
1
A: Envelope glycoprotein B
hetero molecules

A: Envelope glycoprotein B
hetero molecules

A: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,69018
Polymers236,7103
Non-polymers3,98015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area40790 Å2
ΔGint-160 kcal/mol
Surface area80310 Å2
MethodPISA
2
B: Envelope glycoprotein B
hetero molecules

B: Envelope glycoprotein B
hetero molecules

B: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,36415
Polymers236,7103
Non-polymers2,65412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area39760 Å2
ΔGint-138 kcal/mol
Surface area78920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.432, 117.432, 160.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Envelope glycoprotein B / gB / gB-1 / gB1


Mass: 78903.320 Da / Num. of mol.: 2 / Fragment: Ectodomain (UNP residues 30 to 730) / Mutation: A549T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: KOS / Gene: gB, UL27 / Plasmid: PVT-BAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P06437
#2: 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
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT HSV-1 STRAIN KOS SEQUENCE IN THE UNP DATABASE CONTAINS THREE MUTATIONS RELATIVE ...AUTHORS STATE THAT HSV-1 STRAIN KOS SEQUENCE IN THE UNP DATABASE CONTAINS THREE MUTATIONS RELATIVE TO SEQUENCES OF OTHER STRAINS OF HSV-1 AND HSV-2. THEIR SEQUENCE WAS DERIVED FROM THE SEQUENCE OF HSV-1 KOS GB FROM PLASMID PKBXX (S. PERSON) AND DOES NOT CONTAIN THESE MUTATIONS.

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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: 4.05 Å3/Da / Density % sol: 69.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 4000, 0.3 M NaCl, 0.1 M Sodium Citrate, pH 5.5, vapor diffusion, hanging drop, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2012
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. all: 48338 / Num. obs: 48077 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
3.02-3.134.3196
3.13-3.256.4199.80.821
3.25-3.4811000.637
3.4-3.588.611000.427
3.58-3.88.611000.285
3.8-4.18.511000.18
4.1-4.518.611000.12
4.51-5.168.611000.092
5.16-6.58.811000.086
6.5-508.711000.048

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1391refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.0255→48.473 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8016 / SU ML: 0.46 / σ(F): 0.17 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 2261 5.02 %
Rwork0.2007 42746 -
obs0.2028 45007 93.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 253.68 Å2 / Biso mean: 99.743 Å2 / Biso min: 36.36 Å2
Refinement stepCycle: LAST / Resolution: 3.0255→48.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9761 0 141 31 9933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610175
X-RAY DIFFRACTIONf_angle_d0.87713836
X-RAY DIFFRACTIONf_chiral_restr0.0571528
X-RAY DIFFRACTIONf_plane_restr0.0041795
X-RAY DIFFRACTIONf_dihedral_angle_d12.9533684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0255-3.09120.37811110.3622072218372
3.0912-3.16310.35031300.32112358248882
3.1631-3.24220.3931270.30112435256286
3.2422-3.32990.36581360.29842535267188
3.3299-3.42780.36681380.27122631276991
3.4278-3.53840.28651480.25432633278193
3.5384-3.66480.34311480.23942717286595
3.6648-3.81150.26811480.22612749289796
3.8115-3.98490.22341480.19462769291796
3.9849-4.19490.23231470.18052781292898
4.1949-4.45750.18891490.162805295498
4.4575-4.80140.20721470.15452822296999
4.8014-5.28410.15681410.15752876301799
5.2841-6.04750.25841550.18492855301099
6.0475-7.61440.24271430.19952854299799
7.6144-48.47890.19981450.17332854299999
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)
10.2842-0.1425-0.16370.4220.01373.73210.00320.00990.0072-0.05310.0619-0.1074-0.6248-0.0548-0.03990.3284-0.07010.00390.35850.04050.639561.2339-29.151155.2326
22.0163-0.6885-0.32033.1778-0.68383.7845-0.18250.19620.3229-0.37960.31940.2087-1.4544-1.1981-0.0191.41520.2245-0.13291.06390.10040.61547.2506-23.1545-14.7085
31.9971-0.19991.32572.14320.82611.4147-0.19820.34620.3617-0.36080.19080.5233-0.8972-2.10130.01591.15120.3607-0.1492.02540.20810.715139.8516-28.8868-12.2563
41.0533-0.0027-0.67320.81341.74582.77060.12830.31640.311-0.6605-0.2014-0.0265-2.0439-0.67770.20851.3910.2926-0.0290.54340.12260.735150.701-12.176821.6546
50.8627-0.1208-0.02540.20230.14343.2222-0.0798-0.19330.03010.16490.0034-0.0851-0.50760.08510.10320.485-0.0976-0.04980.3261-0.04860.637764.6159-30.96480.3796
63.09580.9408-1.72132.20960.31913.7566-0.41-0.5981-0.00990.14470.32810.25680.4265-0.2448-0.04340.96990.17560.03340.8420.23070.797163.8731-54.9259110.7369
70.06840.09740.47570.1797-0.70315.6212-0.01750.1128-0.2144-0.2190.00970.02411.81620.50420.13090.75130.15380.02030.498-0.07820.676961.0642-45.914135.0869
82.75380.95010.21865.0899-2.34022.7219-0.11190.28210.334-0.0903-0.07470.0726-0.410.36090.18430.6734-0.0652-0.01290.71860.03430.803374.773545.055461.5912
90.141-0.09741.07920.71080.77824.54480.0721-0.351-0.0940.5777-0.00380.08691.5774-1.61970.00341.0856-0.34130.13391.00970.07180.652148.256223.0609161.1665
100.87240.56351.48112.11160.88863.06450.0775-0.6856-0.68870.0827-0.2951-0.14042.6541-1.6868-0.0582.6587-0.6643-0.04660.87860.090.513948.84638.5963158.1544
110.25880.10090.20910.37260.05793.9483-0.0614-0.0659-0.27260.0421-0.1544-0.10641.3409-0.21670.23480.75260.00380.00830.29540.00110.654857.737117.1728105.7332
126.8505-0.9974-0.03463.2692-0.51953.03090.16731.17580.6482-0.6491-0.0779-0.2537-0.29340.4770.04340.9892-0.24270.06060.91970.20860.876472.856555.009749.8084
130.4660.0705-0.66410.0682-0.71434.1004-0.0939-0.01640.19660.1968-0.11990.0376-1.29910.07460.12070.7769-0.086-0.03420.297-0.0280.703560.48449.4685103.3964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 103 through 174 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 226 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 263 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 447 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 448 through 612 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 613 through 658 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 659 through 724 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 103 through 130 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 131 through 294 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 295 through 355 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 356 through 572 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 573 through 629 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 630 through 724 )B0

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