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- PDB-4nry: Crystal Structure of HIV-1 Neutralizing Antibody m66 -

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Basic information

Entry
Database: PDB / ID: 4nry
TitleCrystal Structure of HIV-1 Neutralizing Antibody m66
Components
  • m66 Heavy Chain
  • m66 Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Neutralizing Antibody / HIV-1 gp41 / Membrane Proximal External Region / MPER
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 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 1.1Feb 12, 2014Group: Other
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 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 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: m66 Heavy Chain
B: m66 Heavy Chain
H: m66 Light Chain
A: m66 Light Chain


Theoretical massNumber of molelcules
Total (without water)98,1494
Polymers98,1494
Non-polymers00
Water00
1
L: m66 Heavy Chain
H: m66 Light Chain


Theoretical massNumber of molelcules
Total (without water)49,0752
Polymers49,0752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: m66 Heavy Chain
A: m66 Light Chain


Theoretical massNumber of molelcules
Total (without water)49,0752
Polymers49,0752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.501, 100.724, 166.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Antibody m66 Heavy Chain


Mass: 23762.229 Da / Num. of mol.: 2
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)
#2: Antibody m66 Light Chain


Mass: 25312.398 Da / Num. of mol.: 2
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)

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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: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 52.5% polyethylene glycol 400, 0.2 M calcium acetate, 0.1 M acetate, pH 4.5, 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 / Date: Jun 19, 2010
RadiationMonochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. obs: 26613 / % possible obs: 91.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.2
Reflection shellResolution: 3.14→3.24 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.521 / % possible all: 50.3

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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 7FAB
Resolution: 3.14→44.84 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 29.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1372 5.08 %
Rwork0.228 --
obs0.229 25306 88.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.44 Å2
Refinement stepCycle: LAST / Resolution: 3.14→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6439 0 0 0 6439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036601
X-RAY DIFFRACTIONf_angle_d0.7468969
X-RAY DIFFRACTIONf_dihedral_angle_d11.9742355
X-RAY DIFFRACTIONf_chiral_restr0.0491009
X-RAY DIFFRACTIONf_plane_restr0.0041135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1143-3.22550.4679640.34391199X-RAY DIFFRACTION42
3.2255-3.35460.3528760.32081836X-RAY DIFFRACTION63
3.3546-3.50730.30251270.2852397X-RAY DIFFRACTION85
3.5073-3.69210.29831710.27872745X-RAY DIFFRACTION97
3.6921-3.92330.3041330.26162846X-RAY DIFFRACTION99
3.9233-4.2260.28331730.22682845X-RAY DIFFRACTION100
4.226-4.65090.22051510.19452876X-RAY DIFFRACTION100
4.6509-5.32290.23341530.18662895X-RAY DIFFRACTION100
5.3229-6.70270.23951550.22532943X-RAY DIFFRACTION100
6.7027-44.84560.22281690.21393049X-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)
1-0.03740.022-0.0340.01940.02990.01270.06650.525-0.8064-0.43910.06080.4277-0.00930.0411-00.5820.0136-0.05490.5903-0.09940.5405-60.09111.15546.6481
2-0.02970.06350.02750.01110.10490.0714-0.1103-0.26340.06430.2270.09940.0937-0.1549-0.2726-00.3865-0-0.00870.6716-0.12930.4752-61.26268.526515.1579
30.1210.16950.00960.12910.00760.0522-0.1181-0.0839-0.3221-0.4965-0.09780.1658-0.3981-0.350600.44350.0589-0.06980.5905-0.19860.4412-63.4778.481811.2744
40.0739-0.284-0.04760.2282-0.0967-0.09950.23820.0731-0.8422-1.27251.39040.29950.4324-0.34690-0.3768-0.07492.09580.5879-0.6923-2.4509-32.148815.28880.7619
50.07360.00410.00570.03920.11010.02510.0097-0.12190.0045-0.67770.3335-0.4404-0.2278-0.6901-00.805-0.13680.24460.7985-0.25020.6883-33.086610.8539-0.5038
6-0.01820.0343-0.0018-0.04890.0236-0.0245-0.0178-0.0976-0.03550.0640.1176-0.35320.22460.1589-0-1.2646-1.37432.60110.4080.392-0.2028-17.131411.41920.993
7-0.01040.064-0.0116-0.0910.0448-0.0106-0.45840.40680.26-0.3778-0.9684-0.51330.30270.225-00.1944-0.77812.58921.1386-0.6001-1.4438-24.317214.1076-9.0259
80.03980.0793-0.00450.04820.04670.05730.2101-0.24650.0922-0.2826-0.1306-0.3725-0.62240.163400.67010.0066-0.040.5603-0.02530.5388-43.743316.205329.4644
90.16270.14040.04740.1237-0.13070.1525-0.16350.251-0.14970.2395-0.2176-0.0711-0.560.067300.37090.21250.11720.4798-0.26430.3524-54.863313.168728.4875
10-0.0094-0.00740.0080.0052-0.01210.0178-0.0406-0.2405-0.50830.1303-0.0773-0.1658-0.1223-0.437300.6458-0.0560.13450.4994-0.05050.4715-57.32465.83335.9189
110.0398-0.02510.0008-0.02950.00780.0120.0188-0.509-0.16580.3596-0.3992-0.4098-0.3405-0.408300.49150.06280.06710.4518-0.01910.4752-48.860812.231235.3915
120.02180.04240.00780.10060.0180.0435-0.4150.0221-0.2856-0.7888-0.2053-0.8716-0.2899-0.289200.39480.1202-0.14810.6676-0.2493-0.0659-61.708813.652323.9099
13-0.0103-0.0473-0.0522-0.0121-0.0276-0.02-0.1081-0.1138-0.01850.1646-0.0447-0.3501-0.1273-0.2257-00.339-0.1027-0.12380.46930.05330.5155-35.337312.446825.7456
14-0.00520.03760.02370.03040.0003-0.001-0.5589-0.2957-0.4422-0.2750.1005-0.2298-0.03950.3222-00.3999-0.64240.515-0.35790.36270.5092-26.063820.87029.7536
150.05930.1170.05860.0209-0.00540.0574-0.03590.134-0.4093-0.5171-0.1448-0.381-0.7747-0.2457-00.3453-0.2390.00980.59880.06790.6012-34.109918.104812.6295
160.06350.021-0.00370.010.00240.02680.01390.3049-0.3051-0.050.2365-0.1417-0.40520.157500.5594-0.09790.07990.7423-0.0210.4074-31.563127.27243.6848
170.02380.09050.03720.0050.03470.0153-0.025-0.17110.0271-0.08490.28440.2926-0.3023-0.190100.4469-0.15890.03440.5209-0.01580.4751-29.466726.061116.0002
180.04390.0104-0.0052-0.00520.02890.0087-0.2855-0.18140.09370.3602-0.3808-0.39410.26240.03700.6368-0.0052-0.08420.523-0.03060.4959-1.31560.012335.3425
190.0119-0.0094-0.03010.02560.04540.0186-0.53360.21960.2371-0.2309-0.4155-0.0217-0.27120.0482-01.04970.1241-0.38930.05080.12290.7071-5.077365.656425.6645
200.0252-0.05550.01190.02240.02010.0744-0.03990.00260.02460.2439-0.0720.2621-0.6163-0.208200.89190.1254-0.23790.5324-0.05910.6735-11.711163.957832.0342
21-0.00850.06370.0234-0.01630.01270.012-0.3399-0.1796-0.0842-0.4242-0.095-0.3426-0.0572-0.1369-00.50620.0601-0.22040.4054-0.02090.5056-10.330957.235835.0737
220.0276-0.0003-0.02790.00010.00640.00250.1564-0.0974-0.1077-0.02830.1982-0.1359-0.04510.2024-00.4662-0.1636-0.11380.10790.18670.8324-2.711563.181619.5901
230.0014-0.02380.0195-0.0124-0.0476-0.00760.1939-0.29530.6531-0.0026-0.1729-0.35430.047-0.2569-00.7948-0.0891-0.13570.36930.08540.379-8.704246.71745.7644
24-0.0008-0.0058-0.00320.01670.01220.00310.1181-0.2662-0.50560.12870.2132-0.5183-0.15550.0389-00.5781-0.1548-0.16790.71120.11770.7334-14.758325.976238.8081
25-0.0128-0.00250.00670.0069-0.0197-0.00890.1217-0.08570.3820.12590.2007-0.59010.04370.0581-00.871-0.0267-0.11970.53210.13960.8349-5.493823.583840.1259
26-0.0012-0.01330.01140.0193-0.00340.00040.2135-0.0528-0.01160.26360.2060.0612-0.2168-0.1595-00.5369-0.1605-0.10691.05150.10880.598-14.107943.876641.2953
27-0.03430.00970.00320.00160.0079-0.04420.26410.0827-0.1487-0.03720.18290.05370.44150.275700.82-0.4861-0.2562-1.61581.20260.4737-10.092216.692438.667
280.00470.0333-0.0099-0.0045-0.01470.0185-0.2457-0.2569-0.19020.1562-0.1192-0.0496-0.09370.217501.2544-0.2114-0.26880.45210.06690.7448-10.995624.422349.9717
29-0.0058-0.01370.00850.0141-0.04110.0047-0.4193-0.0779-0.3537-0.34830.0537-0.1661-0.061-0.629300.69150.0137-0.08140.5650.02040.5315-16.281444.394611.9049
300.09050.0952-0.10920.07670.08220.1233-0.19420.04110.089-0.07820.188-0.1718-0.1255-0.229400.68580.1835-0.18180.54310.10870.5607-13.501855.519213.3994
310.0118-0.0228-0.0293-0.0258-0.01380.0109-0.26310.0942-0.4073-0.3197-0.0812-0.8153-0.4763-0.105500.7606-0.0396-0.02850.83320.06360.8582-6.324158.84475.9464
32-0.00820.01460.01880.05060.02180.0201-0.39930.03520.0309-0.43610.05530.0466-0.22920.170300.62760.0276-0.03420.55010.13280.5375-12.261649.89716.2584
330.02530.03150.05050.00870.02030.0006-0.97960.0791-0.5364-0.1542-0.4712-0.2882-0.0272-0.154600.52380.0999-0.4390.43140.010.1961-14.168562.269418.3566
340.0640.21690.0336-0.19190.06660.04950.2996-0.5763-0.4197-1.4329-0.73190.1018-0.39090.06840-0.043-0.2710.0050.48550.06090.6795-17.246930.335925.5576
350.00990.01980.0183-0.00710.0330.0065-0.2147-0.11270.01460.18810.03290.1331-0.2745-0.235700.3651-0.16250.04350.4040.20770.509-20.943135.221525.2563
360.00950.00820.0055-0.01220.00450.0097-0.2334-0.2771-0.21710.1513-0.0108-0.4455-0.1948-0.2379-00.1938-0.18050.20150.51970.00780.7332-15.277333.298330.7506
370.02340.0956-0.01590.20650.03950.028-0.2722-0.24190.19670.00580.1919-0.1158-0.1522-0.282500.3175-0.12150.05880.60660.06570.4831-26.110729.89731.1822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN L AND RESID 1:25 )
2X-RAY DIFFRACTION2(CHAIN L AND RESID 26:48 )
3X-RAY DIFFRACTION3(CHAIN L AND RESID 49:101 )
4X-RAY DIFFRACTION4(CHAIN L AND RESID 102:128 )
5X-RAY DIFFRACTION5(CHAIN L AND RESID 129:174 )
6X-RAY DIFFRACTION6(CHAIN L AND RESID 175:197 )
7X-RAY DIFFRACTION7(CHAIN L AND RESID 198:213 )
8X-RAY DIFFRACTION8(CHAIN H AND RESID 1:17 )
9X-RAY DIFFRACTION9(CHAIN H AND RESID 18:52 )
10X-RAY DIFFRACTION10(CHAIN H AND RESID 53:67 )
11X-RAY DIFFRACTION11(CHAIN H AND RESID 68:87 )
12X-RAY DIFFRACTION12(CHAIN H AND RESID 88:103 )
13X-RAY DIFFRACTION13(CHAIN H AND RESID 104:119 )
14X-RAY DIFFRACTION14(CHAIN H AND RESID 120:145 )
15X-RAY DIFFRACTION15(CHAIN H AND RESID 146:175 )
16X-RAY DIFFRACTION16(CHAIN H AND RESID 176:194 )
17X-RAY DIFFRACTION17(CHAIN H AND RESID 195:214 )
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 39:75 )
21X-RAY DIFFRACTION21(CHAIN B AND RESID 76:90 )
22X-RAY DIFFRACTION22(CHAIN B AND RESID 91:101 )
23X-RAY DIFFRACTION23(CHAIN B AND RESID 102:113 )
24X-RAY DIFFRACTION24(CHAIN B AND RESID 114:144 )
25X-RAY DIFFRACTION25(CHAIN B AND RESID 145:163 )
26X-RAY DIFFRACTION26(CHAIN B AND RESID 164:174 )
27X-RAY DIFFRACTION27(CHAIN B AND RESID 175:197 )
28X-RAY DIFFRACTION28(CHAIN B AND RESID 198:211 )
29X-RAY DIFFRACTION29(CHAIN A AND RESID 1:17 )
30X-RAY DIFFRACTION30(CHAIN A AND RESID 18:53 )
31X-RAY DIFFRACTION31(CHAIN A AND RESID 54:67 )
32X-RAY DIFFRACTION32(CHAIN A AND RESID 68:91 )
33X-RAY DIFFRACTION33(CHAIN A AND RESID 92:120 )
34X-RAY DIFFRACTION34(CHAIN A AND RESID 121:162 )
35X-RAY DIFFRACTION35(CHAIN A AND RESID 163:174 )
36X-RAY DIFFRACTION36(CHAIN A AND RESID 175:192 )
37X-RAY DIFFRACTION37(CHAIN A AND RESID 193:232 )

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