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Basic information

Entry
Database: PDB / ID: 6w5y
TitleInferred receptor binding domain of human endogenous retrovirus envelope EnvP(b)1
ComponentsEnvP(b)1 inferred receptor binding domain
KeywordsVIRAL PROTEIN / Endogenous retrovirus envelope
Biological speciesGammaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMcCarthy, K.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081842 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109740 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI059371 United States
CitationJournal: Mbio / Year: 2020
Title: Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues.
Authors: McCarthy, K.R. / Timpona, J.L. / Jenni, S. / Bloyet, L.M. / Brusic, V. / Johnson, W.E. / Whelan, S.P.J. / Robinson-McCarthy, L.R.
History
DepositionMar 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EnvP(b)1 inferred receptor binding domain
B: EnvP(b)1 inferred receptor binding domain
C: EnvP(b)1 inferred receptor binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22912
Polymers67,0953
Non-polymers2,1349
Water1,51384
1
A: EnvP(b)1 inferred receptor binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1364
Polymers22,3651
Non-polymers7713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EnvP(b)1 inferred receptor binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1204
Polymers22,3651
Non-polymers7553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: EnvP(b)1 inferred receptor binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9744
Polymers22,3651
Non-polymers6093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)243.310, 37.350, 66.990
Angle α, β, γ (deg.)90.000, 102.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein EnvP(b)1 inferred receptor binding domain


Mass: 22365.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gammaretrovirus / Gene: env / Cell line (production host): 293F / Production host: Homo sapiens (human)

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Sugars , 3 types, 3 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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.: 1
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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Non-polymers , 2 types, 90 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5 M Sodium chloride, 0.1 M Bis- tris(hydroxymethyl)aminomethane propane pH 7.0, 20 %(w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.5→49.561 Å / Num. obs: 20893 / % possible obs: 99.85 % / Redundancy: 4.9 % / Biso Wilson estimate: 41.15 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1271 / Rpim(I) all: 0.06285 / Rrim(I) all: 0.1422 / Net I/σ(I): 12.65
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 5 % / Rmerge(I) obs: 0.8862 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 2023 / CC1/2: 0.752 / CC star: 0.927 / Rpim(I) all: 0.4418 / Rrim(I) all: 0.993 / % possible all: 99.75

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→49.561 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.28
RfactorNum. reflection% reflection
Rfree0.2538 1012 4.85 %
Rwork0.222 --
obs0.2237 20882 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.82 Å2 / Biso mean: 56.1702 Å2 / Biso min: 17.71 Å2
Refinement stepCycle: final / Resolution: 2.5→49.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 141 84 4008
Biso mean--93.95 42.86 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084055
X-RAY DIFFRACTIONf_angle_d0.9885563
X-RAY DIFFRACTIONf_dihedral_angle_d4.6422394
X-RAY DIFFRACTIONf_chiral_restr0.048633
X-RAY DIFFRACTIONf_plane_restr0.007704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.63160.34311340.31452765
2.6316-2.79640.31011450.28752814
2.7964-3.01230.32291490.27182795
3.0123-3.31540.31141500.24482828
3.3154-3.7950.25061360.21652841
3.795-4.78070.20871370.18092884
4.7807-49.5610.21961610.19762943
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)
12.3586-1.26450.39232.3627-0.36443.1096-0.3193-0.5790.82230.536-0.2671-0.8382-0.43630.50020.21070.359-0.0574-0.09970.49330.01920.4628-35.7282-7.930949.8627
21.8754-1.0005-0.24792.3999-0.33583.4125-0.19760.067-0.00880.42050.160.10190.242-0.53330.10440.3491-0.0189-0.01910.3271-0.0240.2449-54.1886-14.542153.3366
34.0783-0.607-0.09744.8253-2.98256.6363-0.22660.11480.4002-0.4479-0.11720.00260.2552-0.02720.33140.2023-0.0257-0.00640.2724-0.04270.2984-47.698-11.699639.3104
41.9461-1.06931.00243.9995-2.12633.43940.17870.1199-0.0092-0.11460.05980.0199-0.1031-0.0914-0.09050.33850.01370.03370.2739-0.02210.2774-49.4037-14.208135.4776
55.68991.5428-3.43386.1281-5.1916.1869-0.51530.509-0.6166-0.0544-0.7259-0.68010.26680.2960.55780.3920.0314-0.01490.277-0.05980.2517-44.1903-25.76136.6356
65.0342-1.7157-0.92621.77151.73673.4363-0.2165-0.87410.16760.33290.22830.01560.37650.59780.18790.3117-0.04330.00250.17430.02760.2073-46.1979-17.969250.9336
75.0453-0.45841.62412.29050.1952.7021-0.47380.13110.69780.6056-0.0792-0.7386-0.10220.8368-0.02280.34540.00620.01170.3610.09120.4926-31.3842-11.109541.6287
89.27281.7671.36724.98741.26022.7757-0.1903-0.10340.1881-0.2387-0.061-0.0661-0.1923-0.08780.09890.28410.0198-0.00190.30080.00940.2088-50.6292-12.450243.3617
92.6746-0.2241.15160.0187-0.09690.4855-0.08630.87561.36590.1224-0.1955-0.03310.46970.0139-0.07040.4692-0.0397-0.06950.5233-0.08921.0243-22.20441.937946.1552
108.5197-4.97615.51554.9013-4.80856.8649-0.5898-0.36160.830.19270.7379-0.0254-0.1278-0.8820.04610.37050.1244-0.06840.3509-0.09210.1602-60.581-0.569322.5154
111.63491.8793-0.14844.09440.78793.6335-0.0704-0.0188-0.02510.31450.2748-0.66550.14190.4212-0.20520.34510.0587-0.00210.3773-0.08210.3381-40.78310.60921.7457
122.6318-0.01860.91083.3511.52963.799-0.00060.0827-0.4101-0.2379-0.088-0.32160.59690.134-0.02780.33350.01160.03170.3564-0.02320.2374-48.1521-12.067413.6162
134.02652.2782-1.19936.4822-1.12212.9658-0.5361.00190.2323-1.26450.43511.1635-0.0364-0.32850.14460.38980.0558-0.0930.6455-0.06080.2465-49.1932-5.65312.3595
143.6526-0.9884-1.06041.15280.34021.29540.01850.41030.33310.03670.04050.0913-0.0988-0.0706-0.10040.28960.012-0.01730.33440.03280.1476-52.75950.390115.7813
157.31320.7529-1.33511.56970.25790.9755-0.53510.0513-0.49250.03620.341-0.36760.20630.218-0.0480.3211-0.03390.00910.3558-0.09130.2018-42.6578-8.093214.9093
161.9404-1.9422-0.03921.64750.03850.84-0.2151-0.2257-0.8985-0.03020.21910.40980.5693-0.27670.0190.3516-0.0352-0.02630.360.03020.3656-65.2712-7.314924.8193
178.73463.83250.98825.01060.11711.1706-0.43580.58721.13290.1249-0.4912-0.7333-0.81190.6223-1.89190.3945-0.72940.32221.19190.26861.1925-80.2515-10.806540.793
189.1886-1.02691.76651.95970.40060.4814-0.10540.1311-0.3404-0.2823-0.0191-0.5799-0.14060.19430.13150.37240.02-0.05840.4145-0.00250.8063-6.477-6.515214.948
198.36250.54540.3951.07321.03460.9001-0.091-0.49420.26270.21340.0602-0.1921-0.0536-0.05290.03310.36490.012-0.08550.46130.00270.7377-8.8841-3.697819.9581
201.54450.9252-0.40760.7841-0.53210.4141-0.48622.2317-0.3771-0.38850.37450.2124-0.28130.37350.01820.3336-0.0706-0.01020.6187-0.15610.7611-11.7584-8.103210.4476
210.7166-0.1424-1.39290.1085-0.05133.0101-0.19270.55390.0017-0.23470.6356-1.00590.41390.0498-0.57960.6073-0.14590.03530.843-0.21510.7516-30.4007-9.7531-0.0923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 14 )A3 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 38 )A15 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 52 )A39 - 52
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 69 )A53 - 69
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 80 )A70 - 80
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 112 )A81 - 112
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 126 )A113 - 126
8X-RAY DIFFRACTION8chain 'A' and (resid 127 through 147 )A127 - 147
9X-RAY DIFFRACTION9chain 'A' and (resid 148 through 156 )A148 - 156
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 14 )B3 - 14
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 38 )B15 - 38
12X-RAY DIFFRACTION12chain 'B' and (resid 39 through 69 )B39 - 69
13X-RAY DIFFRACTION13chain 'B' and (resid 70 through 80 )B70 - 80
14X-RAY DIFFRACTION14chain 'B' and (resid 81 through 125 )B81 - 125
15X-RAY DIFFRACTION15chain 'B' and (resid 126 through 139 )B126 - 139
16X-RAY DIFFRACTION16chain 'B' and (resid 140 through 157 )B140 - 157
17X-RAY DIFFRACTION17chain 'B' and (resid 158 through 165 )B158 - 165
18X-RAY DIFFRACTION18chain 'C' and (resid 3 through 69 )D3 - 69
19X-RAY DIFFRACTION19chain 'C' and (resid 70 through 139 )D70 - 139
20X-RAY DIFFRACTION20chain 'C' and (resid 140 through 147 )D140 - 147
21X-RAY DIFFRACTION21chain 'C' and (resid 148 through 164 )D148 - 164

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