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- PDB-4nrx: Crystal Structure of HIV-1 Neutralizing Antibody m66 in complex w... -

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Basic information

Entry
Database: PDB / ID: 4nrx
TitleCrystal Structure of HIV-1 Neutralizing Antibody m66 in complex with gp41 MPER peptide
Components
  • Envelope glycoprotein gp41
  • m66 Heavy Chain
  • m66 Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Neutralizing Antibody / HIV-1 gp41 / Membrane Proximal External Region / MPER
Function / homology
Function and homology information


membrane => GO:0016020 / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsOfek, G. / Yang, Y. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2014
Title: Structural Basis for HIV-1 Neutralization by 2F5-Like Antibodies m66 and m66.6.
Authors: Ofek, G. / Zirkle, B. / Yang, Y. / Zhu, Z. / McKee, K. / Zhang, B. / Chuang, G.Y. / Georgiev, I.S. / O'Dell, S. / Doria-Rose, N. / Mascola, J.R. / Dimitrov, D.S. / Kwong, P.D.
History
DepositionNov 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Envelope glycoprotein gp41
C: Envelope glycoprotein gp41
H: m66 Heavy Chain
A: m66 Heavy Chain
D: m66 Heavy Chain
L: m66 Light Chain
B: m66 Light Chain
E: m66 Light Chain


Theoretical massNumber of molelcules
Total (without water)149,5998
Polymers149,5998
Non-polymers00
Water9,548530
1
P: Envelope glycoprotein gp41
H: m66 Heavy Chain
L: m66 Light Chain


Theoretical massNumber of molelcules
Total (without water)50,6483
Polymers50,6483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Envelope glycoprotein gp41
A: m66 Heavy Chain
B: m66 Light Chain


Theoretical massNumber of molelcules
Total (without water)50,6483
Polymers50,6483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: m66 Heavy Chain
E: m66 Light Chain


Theoretical massNumber of molelcules
Total (without water)48,3032
Polymers48,3032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.262, 93.505, 89.830
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Envelope glycoprotein gp41


Mass: 2345.587 Da / Num. of mol.: 2 / Mutation: E94K / Source method: obtained synthetically / Details: HIV-1 gp41 peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9QQN5
#2: Antibody m66 Heavy Chain


Mass: 25183.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: homo sapiens (human)
#3: Antibody m66 Light Chain


Mass: 23119.521 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 25% isopropanol, 15-20% polyethylene glycol 3350, 0.2 M ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 76772 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 9
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.504 / % possible all: 92

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NRY
Resolution: 2.21→35.02 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 3474 5 %
Rwork0.188 --
obs0.189 76772 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.92 Å2
Refinement stepCycle: LAST / Resolution: 2.21→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10242 0 0 530 10772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910506
X-RAY DIFFRACTIONf_angle_d1.18814278
X-RAY DIFFRACTIONf_dihedral_angle_d13.963744
X-RAY DIFFRACTIONf_chiral_restr0.0711602
X-RAY DIFFRACTIONf_plane_restr0.0061811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0192-2.04210.36281130.29862036X-RAY DIFFRACTION66
2.0421-2.06620.32541450.29962673X-RAY DIFFRACTION85
2.0662-2.09140.37511520.27862671X-RAY DIFFRACTION86
2.0914-2.11780.28441320.25812749X-RAY DIFFRACTION88
2.1178-2.14570.2461270.25532799X-RAY DIFFRACTION89
2.1457-2.17510.27041440.24392835X-RAY DIFFRACTION90
2.1751-2.20610.2521380.24672848X-RAY DIFFRACTION91
2.2061-2.23910.2871550.24912884X-RAY DIFFRACTION92
2.2391-2.2740.27951560.25452928X-RAY DIFFRACTION93
2.274-2.31130.28211600.23252915X-RAY DIFFRACTION93
2.3113-2.35120.25561550.2232948X-RAY DIFFRACTION94
2.3512-2.39390.271570.21632985X-RAY DIFFRACTION95
2.3939-2.43990.24511510.21763035X-RAY DIFFRACTION96
2.4399-2.48970.23251700.21153028X-RAY DIFFRACTION97
2.4897-2.54390.23731570.20413086X-RAY DIFFRACTION98
2.5439-2.6030.24851600.20943073X-RAY DIFFRACTION98
2.603-2.66810.25571760.19813078X-RAY DIFFRACTION98
2.6681-2.74020.20671650.20123083X-RAY DIFFRACTION98
2.7402-2.82080.24271640.23113X-RAY DIFFRACTION98
2.8208-2.91180.23481530.18953066X-RAY DIFFRACTION98
2.9118-3.01580.20531550.18413114X-RAY DIFFRACTION98
3.0158-3.13650.19591690.17973089X-RAY DIFFRACTION98
3.1365-3.27910.24181440.17313108X-RAY DIFFRACTION98
3.2791-3.45190.18931820.17063089X-RAY DIFFRACTION98
3.4519-3.66790.17591750.1593072X-RAY DIFFRACTION98
3.6679-3.95080.23031840.16143093X-RAY DIFFRACTION98
3.9508-4.34770.16141690.14923094X-RAY DIFFRACTION98
4.3477-4.97530.15071450.14023139X-RAY DIFFRACTION98
4.9753-6.26250.191590.17183119X-RAY DIFFRACTION98
6.2625-35.030.20081700.19843177X-RAY DIFFRACTION98
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)
10.1213-0.03960.21920.1918-0.22560.11020.01230.0768-0.00790.0447-0.0109-0.0773-0.02920.0176-00.22870.0316-0.02180.2129-0.01510.2038-49.857834.39613.3236
20.00750.0039-0.01480.00850.02860.0366-0.0902-0.32170.06340.2192-0.0269-0.06920.06520.010500.32910.0686-0.00580.34990.01050.2367-41.703114.643432.333
30.01360.01830.01570.0327-0.0890.0036-0.1214-0.07350.0203-0.06380.0430.007-0.00820.0264-00.26920.05310.00090.27870.00560.2841-41.146514.036525.9046
40.0454-0.00390.01860.00370.01560.0342-0.01490.00670.01850.04730.0317-0.11060.00580.093-00.19350.0080.00720.1997-0.01220.2595-72.123821.853410.4416
50.0135-0.00070.00640.00610.01790.0150.01030.0530.05180.0407-0.0446-0.0083-0.0523-0.0085-00.15670.0298-0.02410.24260.0010.1585-66.98927.31141.3986
60.00530-0.0045-0.0041-0.00080.0062-0.0297-0.0383-0.09490.0027-0.1-0.0608-0.01130.03800.03990.1001-0.09410.34210.00710.19-56.866219.36338.293
70.0731-0.009-0.04860.0264-0.02430.0398-0.00420.0338-0.0271-0.00730.031-0.04240.010.0105-00.16070.0372-0.00390.1579-0.00940.1516-66.024721.00523.5843
80.0003-0.0081-0.0098-0.002200.0055-0.0091-0.1546-0.037-0.0101-0.13490.0632-0.0612-0.1259-00.21850.0025-0.02790.23810.05810.2587-66.31689.888222.736
90.0026-0.0035-0.00220.0139-0.00640.00650.0008-0.0724-0.11730.01710.07660.0695-0.00870.06300.34690.0489-0.00890.48480.03390.2988-40.471412.38539.6329
100.00470.0121-0.0089-0.00630.00790.0146-0.0583-0.0828-0.02270.1430.12090.04380.077-0.0971-00.28640.10340.04810.36460.06160.3034-55.680812.460837.1407
110.00210.03380.0023-0.0010.00850.0031-0.1381-0.03080.06470.0770.09870.0847-0.0117-0.0024-00.4010.2340.13690.4964-0.01790.1744-53.330118.342344.1703
120.00430.00070.00190.0020.00010.0021-0.00680.0345-0.0015-0.05340.0137-0.0027-0.01720.0312-00.30240.0535-0.02430.29740.02010.346-58.793510.327222.1162
130.01220.018-0.01770.00530.03330.0577-0.0896-0.24450.00510.15680.15390.0403-0.074-0.2123-00.34750.0719-0.00540.36840.03610.2551-49.904110.869545.136
140.0623-0.07620.04250.1603-0.02520.1056-0.0891-0.0433-0.04630.01840.0608-0.0611-0.0518-0.0592-00.20440.0204-0.02180.2175-0.0030.1461-17.58690.004328.9582
150.0463-0.0382-0.04710.0134-0.03260.0225-0.1432-0.0667-0.05090.03950.12250.0655-0.0277-0.0585-00.2026-0.00350.01180.2083-0.00660.1869-18.5279-9.994721.9246
160.118-0.0026-0.00880.13840.00550.00180.15330.24090.1807-0.112-0.0303-0.10480.08250.164700.23920.05480.03470.25760.03970.2593-20.601628.49969.3159
170.063-0.0983-0.060.0559-0.01180.08370.02660.02510.0270.02160.0390.01190.02220.015100.18840.0116-0.02740.2240.00120.2326-23.588522.81018.2934
180.0204-0.0206-0.01240.05410.02640.0080.00210.00210.0232-0.0049-0.01010.0174-0.00690.01200.1727-0.01480.00320.1823-0.01030.1595-2.7253-6.0855.401
190.00830.0073-0.0064-0.0014-0.01530.01060.0043-0.0178-0.09280.0124-0.0190.0551-0.00250.010100.11090.0133-0.00310.17720.01120.1651-8.2659-12.160613.7836
200.00510.001-0.00450.00420.00430.01060.08910.00230.0831-0.0632-0.02580.04050.0045-0.0558-00.19710.0280.04340.20620.00560.2521-16.8234-0.95199.8641
210.0173-0.0189-0.03110.00880.02910.072-0.0071-0.00630.01010.0041-0.0328-0.02380.0171-0.0023-00.1409-0.0049-0.0040.1907-0.0040.2002-10.8804-9.43088.1569
220.02540.0150.00820-0.0088-0.0059-0.0209-0.05850.07-0.06780.0274-0.0061-0.02540.0616-00.23780.03490.02750.19830.00980.204-7.59358.0247-5.1254
230.0010.0118-0.01030.0063-0.00270.00080.0664-0.02140.0666-0.0317-0.04010.05620.025-0.018200.23010.01020.03790.2339-0.0050.3326-19.664234.58644.7174
240.0196-0.0069-0.01460.0347-0.01630.0520.05110.12440.1090.08280.0097-0.02820.028-0.049900.22570.0280.02140.18540.01010.318-9.565422.5182-0.6647
25-0.0176-0.0031-0.03650.02440.0067-0.02830.111-0.00820.1623-0.08240.0464-0.1468-0.09480.1723-00.2384-0.03340.05330.16260.0180.3756-10.112734.8326-1.2082
260.21590.0376-0.11350.07440.21590.1113-0.11070.0421-0.16990.16480.02320.1298-0.02730.01400.28940.01110.05310.18040.09550.3985-98.6422.363430.2881
27-0.0526-0.0288-0.1440.03340.0152-0.0187-0.3315-0.28110.978-0.2128-0.15210.40650.45580.2257-00.60150.01350.2040.343-0.0616-0.1847-86.811520.821749.1307
280.0196-0.00740.00380.0005-0.01260.03770.0015-0.0395-0.0117-0.0398-0.0257-0.03220.03910.13100.25340.02270.0240.16820.01480.2767-81.175214.655414.4393
290.0190.0078-0.00840.0084-0.0170.01540.0783-0.0027-0.21050.07510.07010.1164-0.02330.0012-00.17090.0124-0.04750.2148-0.01560.2816-91.782210.042712.8846
300.005-0.0002-0.00010.0047-0.00250.00310.041-0.0993-0.0229-0.03810.03160.0494-0.0170.0379-00.2208-0.0115-0.0040.2705-0.0070.2234-91.633816.617525.843
310.04640.0079-0.0790.02840.030.0287-0.0512-0.0035-0.10490.0040.0558-0.0124-0.0203-0.0045-00.23250.01340.00380.1890.00760.3051-90.191916.055415.4453
32-0.00330.0550.01710.00170.0269-0.0034-0.2428-0.2401-0.2309-0.22670.2990.5226-0.02340.065600.22120.11420.19650.4737-0.1339-0.5841-76.875523.767544.4837
330.01560.00140.00710.0190.00120.0008-0.1299-0.02120.02980.05030.114-0.09650.1090.0813-00.18050.34540.48760.6148-0.2937-0.7392-70.580723.019444.5743
340.0218-0.03890.0113-0.0169-0.04360.0232-0.225-0.29520.30470.511-0.21-0.463-0.36070.3044-00.30470.32170.11560.5647-0.0140.3964-65.75117.761651.8352
350.00270.00550.00040.0028-0.00360.004-0.1622-0.02930.0785-0.0815-0.00630.06960.01040.0149-00.43260.03640.09380.3511-0.02440.3254-79.41924.985233.1378
360.00780.00110.0201-0.0293-0.05010.0011-0.2634-0.12780.21490.1948-0.19810.1123-0.00850.1622-00.35630.2519-0.29981.0704-0.2324-0.7143-68.189424.18954.2943
370.00420.00070.0034-0.00160.00280.00180.0121-0.04510.08630.11950.01120.04660.0146-0.0278-00.28840.0144-0.00040.3314-0.00820.2728-63.429940.0482-8.732
38-0.00040.00250.0003-0.0003-0.00170.00050.0148-0.0369-0.0623-0.0110.00010.0089-0.0740.026200.27620.01660.06140.31130.01950.2397-54.857436.8728-15.9306
390.0001-0.0021-0.0004-0.0002-0.0017-0.00050.0004-0.01280.0080.06270.0155-0.0501-0.01020.009700.39690.03670.05530.28260.0410.3585-10.0253-20.464228.288
400.00070.0007-0.00070.01090.0017-0.00030.01330.0246-0.0124-0.00190.01670.00610.0331-0.0083-00.27690.05320.04690.31860.08240.3418-21.6467-21.895429.164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN H AND RESID 1:111 )
2X-RAY DIFFRACTION2(CHAIN H AND RESID 112:145 )
3X-RAY DIFFRACTION3(CHAIN H AND RESID 146:214 )
4X-RAY DIFFRACTION4(CHAIN L AND RESID 1:25 )
5X-RAY DIFFRACTION5(CHAIN L AND RESID 26:38 )
6X-RAY DIFFRACTION6(CHAIN L AND RESID 39:48 )
7X-RAY DIFFRACTION7(CHAIN L AND RESID 49:101 )
8X-RAY DIFFRACTION8(CHAIN L AND RESID 102:113 )
9X-RAY DIFFRACTION9(CHAIN L AND RESID 114:128 )
10X-RAY DIFFRACTION10(CHAIN L AND RESID 129:150 )
11X-RAY DIFFRACTION11(CHAIN L AND RESID 151:163 )
12X-RAY DIFFRACTION12(CHAIN L AND RESID 164:174 )
13X-RAY DIFFRACTION13(CHAIN L AND RESID 175:213 )
14X-RAY DIFFRACTION14(CHAIN A AND RESID 1:87 )
15X-RAY DIFFRACTION15(CHAIN A AND RESID 88:111 )
16X-RAY DIFFRACTION16(CHAIN A AND RESID 112:134 )
17X-RAY DIFFRACTION17(CHAIN A AND RESID 135:214 )
18X-RAY DIFFRACTION18(CHAIN B AND RESID 1:25 )
19X-RAY DIFFRACTION19(CHAIN B AND RESID 26:38 )
20X-RAY DIFFRACTION20(CHAIN B AND RESID 39:48 )
21X-RAY DIFFRACTION21(CHAIN B AND RESID 49:101 )
22X-RAY DIFFRACTION22(CHAIN B AND RESID 102:113 )
23X-RAY DIFFRACTION23(CHAIN B AND RESID 114:128 )
24X-RAY DIFFRACTION24(CHAIN B AND RESID 129:174 )
25X-RAY DIFFRACTION25(CHAIN B AND RESID 175:212 )
26X-RAY DIFFRACTION26(CHAIN D AND RESID 1:141 )
27X-RAY DIFFRACTION27(CHAIN D AND RESID 142:234 )
28X-RAY DIFFRACTION28(CHAIN E AND RESID 1:25 )
29X-RAY DIFFRACTION29(CHAIN E AND RESID 26:38 )
30X-RAY DIFFRACTION30(CHAIN E AND RESID 39:48 )
31X-RAY DIFFRACTION31(CHAIN E AND RESID 49:101 )
32X-RAY DIFFRACTION32(CHAIN E AND RESID 102:128 )
33X-RAY DIFFRACTION33(CHAIN E AND RESID 129:149 )
34X-RAY DIFFRACTION34(CHAIN E AND RESID 150:163 )
35X-RAY DIFFRACTION35(CHAIN E AND RESID 164:174 )
36X-RAY DIFFRACTION36(CHAIN E AND RESID 175:212 )
37X-RAY DIFFRACTION37(CHAIN P AND RESID 656:663 )
38X-RAY DIFFRACTION38(CHAIN P AND RESID 664:669 )
39X-RAY DIFFRACTION39(CHAIN C AND RESID 656:663 )
40X-RAY DIFFRACTION40(CHAIN C AND RESID 664:668 )

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