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- PDB-5u3l: Crystal Structure of DH511.2 Fab in Complex with HIV-1 gp41 MPER ... -

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Basic information

Entry
Database: PDB / ID: 5u3l
TitleCrystal Structure of DH511.2 Fab in Complex with HIV-1 gp41 MPER 670-683 Peptide
Components
  • DH511.2 Fab Heavy Chain
  • DH511.2 Fab Light Chain
  • gp41 MPER peptide
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 / Neutralizing / Antibody / gp41 / MPER / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.165 Å
AuthorsOfek, G. / Wu, L. / Lougheed, C.S. / Williams, L.D. / Nicely, N.I. / Haynes, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5UM1AII00645 United States
CitationJournal: Sci Immunol / Year: 2017
Title: Potent and broad HIV-neutralizing antibodies in memory B cells and plasma.
Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I. ...Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I.S. / Seaman, M.S. / Parks, R.J. / Marshall, D.J. / Anasti, K. / Yang, G. / Nie, X. / Tumba, N.L. / Wiehe, K. / Wagh, K. / Korber, B. / Kepler, T.B. / Munir Alam, S. / Morris, L. / Kamanga, G. / Cohen, M.S. / Bonsignori, M. / Xia, S.M. / Montefiori, D.C. / Kelsoe, G. / Gao, F. / Mascola, J.R. / Moody, M.A. / Saunders, K.O. / Liao, H.X. / Tomaras, G.D. / Georgiou, G. / Haynes, B.F.
History
DepositionDec 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / software
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
H: DH511.2 Fab Heavy Chain
L: DH511.2 Fab Light Chain
A: DH511.2 Fab Heavy Chain
B: DH511.2 Fab Light Chain
P: gp41 MPER peptide
C: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)102,7156
Polymers102,7156
Non-polymers00
Water3,837213
1
H: DH511.2 Fab Heavy Chain
L: DH511.2 Fab Light Chain
P: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)51,3583
Polymers51,3583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-32 kcal/mol
Surface area21460 Å2
MethodPISA
2
A: DH511.2 Fab Heavy Chain
B: DH511.2 Fab Light Chain
C: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)51,3583
Polymers51,3583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-29 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.072, 75.644, 123.427
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-100-

PHE

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Components

#1: Antibody DH511.2 Fab Heavy Chain


Mass: 25101.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Heavy Chain / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody DH511.2 Fab Light Chain


Mass: 23466.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Light Chain / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Protein/peptide gp41 MPER peptide


Mass: 2789.345 Da / Num. of mol.: 2 / Fragment: gp41 656-683 / Source method: obtained synthetically / Details: gp41 MPER 670-683 Peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q73372*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 8000, 10% PEG 400, 0.5 M NaCl, 0.1 M C2H3NaO2 pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→42.51 Å / Num. obs: 51031 / % possible obs: 93.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 36.98 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.045 / Rrim(I) all: 0.109 / Χ2: 0.93 / Net I/σ(I): 8.3 / Num. measured all: 259846
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
2.17-2.232.60.49834950.815152.5
2.23-2.313.10.5390.785185.2
2.31-2.393.80.5050.859194.2
2.39-2.484.40.4450.895195.8
2.48-2.650.3930.927196.2
2.6-2.735.50.3350.934197.7
2.73-2.915.90.2620.966199.8
2.91-3.1360.1770.9861100
3.13-3.445.90.120.9911100
3.44-3.945.80.0880.9941100
3.94-4.975.80.0650.9961100
4.97-505.70.0570.997199.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U3P
Resolution: 2.165→42.51 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 2611 5.12 %
Rwork0.2048 --
obs0.2061 50955 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.165→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6983 0 0 213 7196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027178
X-RAY DIFFRACTIONf_angle_d0.5549769
X-RAY DIFFRACTIONf_dihedral_angle_d10.4974213
X-RAY DIFFRACTIONf_chiral_restr0.0441080
X-RAY DIFFRACTIONf_plane_restr0.0031239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.165-2.20440.2994650.2721497X-RAY DIFFRACTION56
2.2044-2.24680.27711030.27282037X-RAY DIFFRACTION76
2.2468-2.29260.32151380.26222378X-RAY DIFFRACTION88
2.2926-2.34250.27821490.24672464X-RAY DIFFRACTION94
2.3425-2.3970.2751430.25592559X-RAY DIFFRACTION95
2.397-2.45690.27271350.24152563X-RAY DIFFRACTION95
2.4569-2.52330.26581300.23632572X-RAY DIFFRACTION95
2.5233-2.59760.30131360.24032598X-RAY DIFFRACTION97
2.5976-2.68140.26231700.2372626X-RAY DIFFRACTION98
2.6814-2.77720.23041410.23822638X-RAY DIFFRACTION99
2.7772-2.88840.28931460.23512696X-RAY DIFFRACTION100
2.8884-3.01980.25351280.2262706X-RAY DIFFRACTION100
3.0198-3.1790.23291570.22522687X-RAY DIFFRACTION100
3.179-3.37810.23771420.21062669X-RAY DIFFRACTION100
3.3781-3.63880.22081280.19882723X-RAY DIFFRACTION100
3.6388-4.00470.20151410.18882718X-RAY DIFFRACTION100
4.0047-4.58360.18971390.15842725X-RAY DIFFRACTION100
4.5836-5.77260.19781660.1632712X-RAY DIFFRACTION100
5.7726-42.51830.23031540.2082776X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.17020.64980.2821.7036-0.3851.8838-0.09330.47510.2121-0.07640.0176-0.0592-0.27940.0340.13570.3037-0.0609-0.0340.56170.06170.2826-35.243416.680142.7261
24.4266-2.0748-0.12125.0398-0.0061.3480.05211.1282-0.0567-0.30180.01830.00450.18090.6268-0.0990.37970.028-0.00880.9880.09220.58370.847910.575536.2284
35.8942-2.1573-1.97874.62576.10368.55170.342-0.3362-0.31130.0248-0.147-0.53170.2484-0.2077-0.20870.354-0.0952-0.0520.51910.09510.4551-24.0624-1.878356.9784
44.8469-0.61170.6222.7072-0.76682.6978-0.044-0.2192-0.5230.0423-0.0210.00110.3886-0.2294-0.0570.291-0.0607-0.01570.51670.07390.3793-33.5640.119851.7011
54.3859-1.20110.48483.94680.20892.0513-0.0415-0.1577-0.52370.18610.09060.0390.0755-0.2872-0.050.269-0.10170.00650.56140.10730.359-30.94190.755353.7466
64.6817-4.83091.10755.1497-0.67562.6522-0.28290.1454-0.96910.1336-0.04340.5963-0.25970.04680.31480.44940.0256-0.20020.5059-0.09570.7589-9.6787-8.092851.372
76.82793.49220.72071.79690.35273.0178-0.0491.59890.3588-0.45450.0439-0.0293-0.01120.59360.01120.33090.01570.00461.02280.20450.695610.887912.740443.3539
86.99494.89571.29578.10761.00851.38660.17210.40470.24010.2927-0.09760.52290.04490.109-0.20930.36270.0956-0.02210.68280.03670.50441.63514.65652.5876
99.81773.06394.0565.49911.56682.6013-0.0961.0114-0.08790.03510.28740.59040.03310.4689-0.07860.46640.15050.07260.6880.04730.4627-1.68145.329550.7371
105.77215.42170.83015.62980.87712.3942-0.41160.58280.9257-0.08970.52930.8636-0.23950.5458-0.08750.37890.0211-0.04760.72370.11930.72276.871514.853750.2426
117.94974.84110.86523.8272-1.13513.23790.45040.162-0.76610.6162-0.4269-0.67190.13650.6934-0.12190.52020.0771-0.05180.58780.00460.425710.26984.60856.0196
123.56432.48843.32721.93692.39835.8767-0.13030.1899-0.11420.1140.4198-0.1801-0.13761.252-0.25320.2542-0.05330.02750.6615-0.03690.3213-0.982438.890316.5143
132.1068-0.27130.88711.95422.1836.2323-0.0203-0.0501-0.17790.10780.04210.01050.19010.379-0.01660.3094-0.0304-0.01520.3720.06330.3114-7.785935.829723.1448
143.271-1.4141-0.15884.4355-0.14832.12910.44290.71680.1391-0.8581-0.40690.0581-0.5026-0.4495-0.0270.58720.1350.0450.49280.05110.2635-20.376245.9704-9.3326
153.1264-2.02943.39087.6675-5.10374.94710.51270.66950.6032-0.5681-0.3328-0.5099-1.3557-0.02850.10750.94670.2450.21530.76180.09560.4086-14.719649.5236-15.8292
164.1797-1.8020.94862.6099-0.27757.2434-0.1169-0.24110.11330.1711-0.18180.3704-0.8821-0.75430.19950.38920.0435-0.04080.4101-0.0580.3023-22.105348.173326.3739
178.4845-3.86926.80665.255-6.2818.3225-0.5149-0.9869-0.05890.84230.5661-0.16430.2824-0.25980.04940.57150.2507-0.05330.5489-0.0240.5107-32.860357.95668.2931
181.3125-0.6019-0.18435.23772.23872.59770.50720.7097-0.7428-0.8392-0.17110.7860.23250.17750.40210.71420.2558-0.30490.6822-0.10550.6177-33.324246.2125-9.9155
192.5439-0.9732-0.21953.11581.36612.69880.41820.6768-0.6489-0.5024-0.38181.07370.3135-0.0146-0.00150.64620.1147-0.31080.5268-0.10010.7253-36.475345.713-8.3026
205.8126-0.0704-3.55922.8462-0.96254.1320.0401-0.40690.1170.08610.140.4004-1.13990.1822-0.35860.31680.0075-0.00670.75490.11530.37-56.436512.127749.1453
218.2930.85913.18044.25270.83441.2826-0.01320.6729-0.88071.2623-0.1545-1.9729-0.0780.59450.12840.5055-0.072-0.11250.64360.0980.536.060141.863537.7854
224.80171.3725-2.91973.8417-0.11779.77090.1409-0.0818-0.979-0.0140.0760.13870.9036-0.277-0.32460.3717-0.0563-0.08220.56160.16290.3654-3.860637.691545.2082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 111 )
2X-RAY DIFFRACTION2chain 'H' and (resid 112 through 213 )
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 18 )
4X-RAY DIFFRACTION4chain 'L' and (resid 19 through 61 )
5X-RAY DIFFRACTION5chain 'L' and (resid 62 through 102 )
6X-RAY DIFFRACTION6chain 'L' and (resid 103 through 113 )
7X-RAY DIFFRACTION7chain 'L' and (resid 114 through 128 )
8X-RAY DIFFRACTION8chain 'L' and (resid 129 through 150 )
9X-RAY DIFFRACTION9chain 'L' and (resid 151 through 172 )
10X-RAY DIFFRACTION10chain 'L' and (resid 173 through 188 )
11X-RAY DIFFRACTION11chain 'L' and (resid 189 through 212 )
12X-RAY DIFFRACTION12chain 'A' and (resid 1 through 33 )
13X-RAY DIFFRACTION13chain 'A' and (resid 34 through 111 )
14X-RAY DIFFRACTION14chain 'A' and (resid 112 through 188 )
15X-RAY DIFFRACTION15chain 'A' and (resid 189 through 213 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 102 )
17X-RAY DIFFRACTION17chain 'B' and (resid 103 through 113 )
18X-RAY DIFFRACTION18chain 'B' and (resid 114 through 150 )
19X-RAY DIFFRACTION19chain 'B' and (resid 151 through 211 )
20X-RAY DIFFRACTION20chain 'P' and (resid 668 through 685 )
21X-RAY DIFFRACTION21chain 'C' and (resid 667 through 671 )
22X-RAY DIFFRACTION22chain 'C' and (resid 672 through 685 )

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