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- PDB-4nrz: Crystal Structure of HIV-1 Neutralizing Antibody m66.6 -

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Basic information

Entry
Database: PDB / ID: 4nrz
TitleCrystal Structure of HIV-1 Neutralizing Antibody m66.6
Components
  • M66.6 HEAVY CHAIN
  • M66.6 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: 2.42 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: M66.6 HEAVY CHAIN
A: M66.6 HEAVY CHAIN
L: M66.6 LIGHT CHAIN
B: M66.6 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,62011
Polymers97,1634
Non-polymers4587
Water3,117173
1
H: M66.6 HEAVY CHAIN
L: M66.6 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8436
Polymers48,5812
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: M66.6 HEAVY CHAIN
B: M66.6 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7785
Polymers48,5812
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.160, 118.873, 80.033
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody M66.6 HEAVY CHAIN


Mass: 25183.219 Da / Num. of mol.: 2 / Fragment: Fab Heavy Chain
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 M66.6 LIGHT CHAIN


Mass: 23398.088 Da / Num. of mol.: 2 / Fragment: Fab Light Chain
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% polyethylene glycol 8000, 0.05 M zinc acetate, 0.05 M sodium cacaodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2011
RadiationMonochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 35882 / % possible obs: 85.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 8.2
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.315 / % possible all: 50.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→30.19 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.38 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1543 4.31 %
Rwork0.177 --
obs0.178 35840 84.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.12 Å2
Refinement stepCycle: LAST / Resolution: 2.42→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6719 0 7 173 6899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086894
X-RAY DIFFRACTIONf_angle_d1.1739364
X-RAY DIFFRACTIONf_dihedral_angle_d13.6962468
X-RAY DIFFRACTIONf_chiral_restr0.0661040
X-RAY DIFFRACTIONf_plane_restr0.0061187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4205-2.49860.3063710.23421555X-RAY DIFFRACTION43
2.4986-2.58780.32741070.23522038X-RAY DIFFRACTION56
2.5878-2.69140.29141050.23432392X-RAY DIFFRACTION65
2.6914-2.81380.28631260.23692798X-RAY DIFFRACTION76
2.8138-2.9620.2851420.22883364X-RAY DIFFRACTION90
2.962-3.14740.28381570.21873593X-RAY DIFFRACTION98
3.1474-3.39010.24671680.18773701X-RAY DIFFRACTION100
3.3901-3.73070.2131670.16683674X-RAY DIFFRACTION100
3.7307-4.26930.18781680.1543713X-RAY DIFFRACTION100
4.2693-5.37390.15311770.12873702X-RAY DIFFRACTION100
5.3739-30.19670.1851550.17283767X-RAY DIFFRACTION99
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)
10.0063-0.00350.00540.00070.0005-0.0020.0876-0.02450.0045-0.04040.066-0.0129-0.00760.0714-00.16190.00450.00820.1622-0.04150.198817.9417-42.8172-1.3373
2-0.0053-00.00570.0030.0115-0.01010.0989-0.0001-0.0424-0.03890.07230.01570.0213-0.0361-0-0.5578-0.2004-0.4904-0.369-0.2933-0.369212.6065-43.16027.1813
3-0.0690.00350.1013-0.030.0331-0.05540.0937-0.0765-0.05390.05430.08330.0891-0.12050.10050-0.6261-0.1912-0.7528-0.3888-0.4106-0.82567.4555-37.7557-1.1763
4-0.0036-0.00490.0020.00740.00520.00080.06460.01290.0115-0.04230.0522-0.0733-0.0288-0.029800.17660.0609-0.07030.0407-0.08110.2101-6.0288-51.2545-21.809
50.0016-0.00240.0020.00970.00880.00160.08640.02440.00140.03460.0098-0.04880.0134-0.0368-00.14270.145-0.15070.1162-0.02120.1243-10.2172-47.8497-20.7743
6-0.0015-0.00430.00430.00620.0015-0.00290.04290.03520.0003-0.00510.0482-0.0551-0.0173-0.041800.15840.1019-0.03960.0413-0.12790.2284-6.5732-54.2431-29.3223
70.002-0.0030.00330.00390.00360.002-0.02620.0194-0.0229-0.0226-0.02050.0216-0.02730.035800.0433-0.03350.00410.10250.00060.1768-2.2305-21.3884-55.9983
80.00460.0057-0.0041-0.0020.0014-0.00040.0259-0.0037-0.0487-0.00910.0218-0.00740.01480.0226-0-0.3423-0.1013-0.0995-0.083-0.2481-0.4189-13.6226-22.5715-56.2831
90.0009-0.00070.00010.0009-0.00110.00130.00310.02490.0238-0.00540.00480.00030.0005-0.01400.13910.0018-0.00450.1703-0.00160.1921-18.2315-15.8515-63.3475
100.00210.02330.0068-0.032-0.00050.00290.13940.005-0.0109-0.14820.09840.0226-0.0832-0.03890-0.4125-0.09610.17520.0673-0.0218-0.1002-16.6129-22.799-58.5991
11-0.00410.0184-0.0019-0.02280.00170.00370.1640.0350.0395-0.0606-0.0246-0.0233-0.1304-0.00360-0.254-0.2431-0.2265-0.1112-0.2122-0.0933-1.8096-15.7958-45.1136
120.010.0029-0.0054-0.00270.00030.00070.0008-0.0348-0.0179-0.0222-0.03840.0037-0.00950.0131-0-0.0849-0.0511-0.07310.25280.0030.009111.267-12.3143-34.1794
130.02080.0016-0.01-0.0042-0.00180.00480.04070.0041-0.00260.0320.02670.0087-0.0430.0529-0-0.11190.0291-0.02560.40610.03370.037712.8889-12.2654-30.8076
140.003-0.005-0.0064-0.00030.00350.0037-0.0595-0.01650.0115-0.0616-0.02440.0754-0.0131-0.0054-00.07060.0611-0.00290.1803-0.04270.1035-8.0656-25.65111.615
150.0067-0.00080.00280.004-0.00620.0045-0.01820.088-0.0094-0.00960.0014-0.01-0.02650.033300.1335-0.01940.0896-0.0986-0.2443-0.2272.9938-23.31733.1287
160.0010.00070.00040.001-0.00120.0018-0.03450.01190.0088-0.02630.03480.0088-0.00820.000900.1016-0.0145-0.00750.0847-0.01020.0676-2.1251-18.08985.7699
17-0.0013-0.00210.005-0.0014-0.0036-0.0027-0.02480.0354-0.00390.04380.00030.02930.01920.0071-0-0.118-0.0579-0.2502-0.02760.0308-0.29810.6525-27.21121.8069
18-00.00240.00130.0002-0.00090.0004-0.0011-0.00780.00280.0141-0.01310.0107-0.01780.0151-00.0458-0.0899-0.06440.07560.01590.0954-15.3186-28.7548-11.7265
190.00310.003-0.00180.0012-0.00110.0018-0.00430.0003-0.0111-0.004-0.0098-0.0074-0.0185-0.002400.1929-0.028-0.03950.0947-0.12440.237-18.1828-57.8795-20.1946
20-0.00510.00210.00350.00120.00350.0030.0608-0.0105-0.023-0.00630.05730.0061-0.0271-0.0027-00.2373-0.05530.078-0.0768-0.1767-0.0854-20.2529-45.0322-11.9727
21-0.00120.0023-0.0009-0.00110.00010.0008-0.0273-0.0013-0.00830.0222-0.01110.0202-0.0014-0.010400.2257-0.08670.02970.2334-0.040.1053-21.2297-52.5162-6.4268
22-0.0010.0080.02490.004-0.00960.0004-0.00380.0163-0.04840.0714-0.03140.08140.00180.041300.2173-0.06510.0303-0.03340.0510.132-19.2588-49.5318-13.4715
230.00360.0011-0.002500.0016-0.00030.08850.0078-0.0031-0.00210.0540.01470.0069-0.0279-00.2911-0.04220.13490.3039-0.07850.4419-29.3414-47.0496-15.2836
240.0040.0008-0.0045-0.0025-0.0035-0.0001-0.04350.01690.02520.02320.00550.0428-0.00170.0132-00.11520.0282-0.02630.20040.0030.1322-22.9881-13.9846-34.0229
250.0015-0.0013-0.0031-00.00260.0083-0.00090.02160.0017-0.0004-0.0081-0.0160.0201-0.01300.02450.03040.06950.0646-0.0720.0612-24.3443-19.6001-42.036
260.00140.002-0.00010.0014-0.00060.00160.0029-0.01-0.0120.0149-0.006-0.02050.0129-0.0009-00.0782-0.0254-0.0150.174-0.03010.0692-28.513-26.9718-38.8768
27-0.0014-0.0048-0.0013-0.0031-0.00260.0016-0.0049-0.0092-0.02720.0182-0.0309-0.0370.0180.0123-00.0862-0.01090.01420.11580.03140.039-22.9178-23.1928-31.0998
28-0.0001-0.0011-0-0.0038-00.00050.03220.02770.01740.0198-0.0028-0.0112-0.0097-0.02250-0.02480.04050.06410.0026-0.0589-0.0577-23.0129-16.5007-46.769
290.00080.0012-0.0009-0.00170.0011-00.0145-0.01240.01010.00680.02750.00120.0079-0.000400.1162-0.02060.00240.1282-0.03890.1389-12.2967-13.3062-22.8417
30-0.00050.0012-0.00570.0014-0.0031-0.00760.0545-0.0352-0.01550.0120.09520.0318-0.06330.023-00.1116-0.23370.24780.00630.03540.15094.8784-0.4988-27.4982
31-0.00070.0004-0.00190.00020.00020.0014-0.0135-0.00940.0024-0.0104-0.0047-0.00280.0277-0.0025-00.22040.01770.08850.083-0.02260.15870.29426.167-32.3463
320.00050.0001-0.00010.00080.00020.00060.0013-0.00080.00250.00530.0164-0.00030.00180.0154-00.1469-0.00440.04170.07690.10780.0754-4.7598-16.1804-25.0626
330.0005-0.0006-0.00420.00110.00180.0002-0.0223-0.00530.00880.016-0.005-0.00820.00830.0053-00.2726-0.050.14740.0759-0.01340.15589.53557.1083-33.4098
340.0021-0.0032-0.0050.00350.0035-0.0005-0.0027-0.0106-0.00920.01530.01340.00990.01140.00100.2285-0.04710.22670.1035-0.00770.27592.57887.5284-24.2455
350.0009-0.0003-0.00360.0030.0053-0.00430.013-0.0116-0.01040.00080.0340.0265-0.01770.0036-00.3609-0.09820.14410.3028-0.13920.48271.56374.8922-19.1777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:32 )H1 - 32
2X-RAY DIFFRACTION2( CHAIN H AND RESID 33:87 )H33 - 87
3X-RAY DIFFRACTION3( CHAIN H AND RESID 88:134 )H88 - 134
4X-RAY DIFFRACTION4( CHAIN H AND RESID 135:157 )H135 - 157
5X-RAY DIFFRACTION5( CHAIN H AND RESID 158:189 )H158 - 189
6X-RAY DIFFRACTION6( CHAIN H AND RESID 190:214 )H190 - 214
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1:17 )A1 - 17
8X-RAY DIFFRACTION8( CHAIN A AND RESID 18:52 )A18 - 52
9X-RAY DIFFRACTION9( CHAIN A AND RESID 53:66 )A53 - 66
10X-RAY DIFFRACTION10( CHAIN A AND RESID 67:100 )A67 - 100
11X-RAY DIFFRACTION11( CHAIN A AND RESID 101:134 )A101 - 134
12X-RAY DIFFRACTION12( CHAIN A AND RESID 135:157 )A135 - 157
13X-RAY DIFFRACTION13( CHAIN A AND RESID 158:214 )A158 - 214
14X-RAY DIFFRACTION14( CHAIN L AND RESID 1:18 )L1 - 18
15X-RAY DIFFRACTION15( CHAIN L AND RESID 19:61 )L19 - 61
16X-RAY DIFFRACTION16( CHAIN L AND RESID 62:75 )L62 - 75
17X-RAY DIFFRACTION17( CHAIN L AND RESID 76:101 )L76 - 101
18X-RAY DIFFRACTION18( CHAIN L AND RESID 102:113 )L102 - 113
19X-RAY DIFFRACTION19( CHAIN L AND RESID 114:128 )L114 - 128
20X-RAY DIFFRACTION20( CHAIN L AND RESID 129:150 )L129 - 150
21X-RAY DIFFRACTION21( CHAIN L AND RESID 151:163 )L151 - 163
22X-RAY DIFFRACTION22( CHAIN L AND RESID 164:197 )L164 - 197
23X-RAY DIFFRACTION23( CHAIN L AND RESID 198:213 )L198 - 213
24X-RAY DIFFRACTION24( CHAIN B AND RESID 1:18 )B1 - 18
25X-RAY DIFFRACTION25( CHAIN B AND RESID 19:48 )B19 - 48
26X-RAY DIFFRACTION26( CHAIN B AND RESID 49:69 )B49 - 69
27X-RAY DIFFRACTION27( CHAIN B AND RESID 70:83 )B70 - 83
28X-RAY DIFFRACTION28( CHAIN B AND RESID 84:101 )B84 - 101
29X-RAY DIFFRACTION29( CHAIN B AND RESID 102:113 )B102 - 113
30X-RAY DIFFRACTION30( CHAIN B AND RESID 114:150 )B114 - 150
31X-RAY DIFFRACTION31( CHAIN B AND RESID 151:163 )B151 - 163
32X-RAY DIFFRACTION32( CHAIN B AND RESID 164:174 )B164 - 174
33X-RAY DIFFRACTION33( CHAIN B AND RESID 175:188 )B175 - 188
34X-RAY DIFFRACTION34( CHAIN B AND RESID 189:198 )B189 - 198
35X-RAY DIFFRACTION35( CHAIN B AND RESID 199:212 )B199 - 212

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