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- PDB-7mfa: Crystal structure of antibody 10E8v4-P100fA+P100gA Fab -

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Basic information

Entry
Database: PDB / ID: 7mfa
TitleCrystal structure of antibody 10E8v4-P100fA+P100gA Fab
Components
  • Antibody 10E8v4 Fab heavy chain
  • Antibody 10E8v4 Fab light chain
KeywordsIMMUNE SYSTEM / Monoclonal antibody 10E8 / MPER / cis-trans isomerization / size-exclusion chromatography
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: Antibodies / Year: 2021
Title: Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography.
Authors: Do Kwon, Y. / Wang, X.E. / Bender, M.F. / Yang, R. / Li, Y. / McKee, K. / Rawi, R. / O'Dell, S. / Schneck, N.A. / Shaddeau, A. / Zhang, B. / Arnold, F.J. / Connors, M. / Doria-Rose, N.A. / ...Authors: Do Kwon, Y. / Wang, X.E. / Bender, M.F. / Yang, R. / Li, Y. / McKee, K. / Rawi, R. / O'Dell, S. / Schneck, N.A. / Shaddeau, A. / Zhang, B. / Arnold, F.J. / Connors, M. / Doria-Rose, N.A. / Kwong, P.D. / Lei, Q.P.
History
DepositionApr 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Antibody 10E8v4 Fab heavy chain
L: Antibody 10E8v4 Fab light chain
C: Antibody 10E8v4 Fab heavy chain
D: Antibody 10E8v4 Fab light chain
G: Antibody 10E8v4 Fab heavy chain
I: Antibody 10E8v4 Fab light chain
M: Antibody 10E8v4 Fab heavy chain
N: Antibody 10E8v4 Fab light chain
Q: Antibody 10E8v4 Fab heavy chain
R: Antibody 10E8v4 Fab light chain
U: Antibody 10E8v4 Fab heavy chain
V: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)288,21812
Polymers288,21812
Non-polymers00
Water1,47782
1
H: Antibody 10E8v4 Fab heavy chain
L: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0362
Polymers48,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-20 kcal/mol
Surface area20550 Å2
MethodPISA
2
C: Antibody 10E8v4 Fab heavy chain
D: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0362
Polymers48,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-19 kcal/mol
Surface area20700 Å2
MethodPISA
3
G: Antibody 10E8v4 Fab heavy chain
I: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0362
Polymers48,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-22 kcal/mol
Surface area21020 Å2
MethodPISA
4
M: Antibody 10E8v4 Fab heavy chain
N: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0362
Polymers48,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-17 kcal/mol
Surface area20600 Å2
MethodPISA
5
Q: Antibody 10E8v4 Fab heavy chain
R: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0362
Polymers48,0362
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-19 kcal/mol
Surface area20650 Å2
MethodPISA
6
U: Antibody 10E8v4 Fab heavy chain
V: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0362
Polymers48,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-22 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.778, 53.795, 328.528
Angle α, β, γ (deg.)90.000, 90.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Antibody 10E8v4 Fab heavy chain


Mass: 25085.928 Da / Num. of mol.: 6 / Mutation: P100fA, P100gA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-15*05 / Plasmid: pVRC8400 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody
Antibody 10E8v4 Fab light chain


Mass: 22950.463 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV3-19*01 / Plasmid: pVRC8400 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10% PEG 8000, 5% Iso-propanol, 0.2M Ammonium sulfate 0.1M HEPES 7.4

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2019
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 108309 / % possible obs: 81.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.073 / Rrim(I) all: 0.17 / Χ2: 1.493 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.442.42.62842320.1091.5493.0790.42163.7
2.44-2.492.62.74546130.1731.5533.1830.42971.1
2.49-2.532.92.4646340.1561.3992.8550.43669.8
2.53-2.593.62.56842150.241.2912.8920.42664.4
2.59-2.644.22.14451660.430.9782.3670.43978.2
2.64-2.74.71.97952510.3980.872.1710.45679.2
2.7-2.774.91.64854500.5530.7191.8070.47282.6
2.77-2.855.11.23453550.6870.531.3490.50380.8
2.85-2.935.10.99354520.7220.4371.090.55883.1
2.93-3.025.10.78454210.8090.3480.8620.59881.7
3.02-3.135.10.62656330.840.2820.690.69484.8
3.13-3.2650.42855480.8990.1940.4730.85684.4
3.26-3.414.80.30556680.9450.1410.3381.13685.2
3.41-3.584.60.23957950.9610.1130.2661.45986.3
3.58-3.814.60.1953500.9740.0920.2121.92480.6
3.81-4.14.80.14463780.9820.0690.1612.51495.8
4.1-4.524.40.10362200.9920.0520.1163.12692.9
4.52-5.174.10.07960050.9940.0410.093.59789.8
5.17-6.514.20.07161160.9940.0360.0813.5389.7
6.51-504.40.05858070.9950.0290.0653.98782.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQ9

5iq9


Resolution: 2.4→35.01 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 40.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2861 1902 1.81 %
Rwork0.2384 103202 -
obs0.2392 105104 78.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.6 Å2 / Biso mean: 99.2728 Å2 / Biso min: 38.5 Å2
Refinement stepCycle: final / Resolution: 2.4→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19637 0 0 82 19719
Biso mean---66.2 -
Num. residues----2599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.450.4586750.40724100417544
2.45-2.520.47961040.39625682578662
2.52-2.590.4198980.37815543564159
2.59-2.670.37871270.36757213734077
2.67-2.770.45571410.34997487762881
2.77-2.880.36081410.32087604774581
2.88-3.010.36661430.30917696783982
3.01-3.170.35521460.29747883802984
3.17-3.370.31661500.27247984813485
3.37-3.630.30431500.25228033818386
3.63-3.990.30081530.23638237839087
3.99-4.570.24411620.19668846900893
4.57-5.750.2351630.19568547871090
5.75-35.010.25091490.20938347849685
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)
11.55720.5797-0.28643.2397-2.15824.7787-0.19720.1749-0.2762-0.6007-0.0888-0.21641.10160.03140.26570.9034-0.12030.01350.4145-0.01350.51359.717-8.15886.382
24.9785-1.45760.55765.51331.76062.96930.0430.24450.7288-0.6101-0.2594-0.26380.00960.78620.19041.069-0.0771-0.18751.10290.22840.64198.75819.7762.103
30.86210.7851-0.02093.017-2.08383.964-0.09260.1388-0.1173-0.3382-0.1708-0.36550.6420.07740.22930.8966-0.0652-0.02360.44780.00450.53957.898-26.86589.559
41.6923-1.7761-0.85789.1812-1.21083.7464-0.07650.2770.40890.1343-0.2697-0.7037-0.39280.160.3131.2226-0.1821-0.27530.84430.16170.58358.1763.35765.033
52.3476-0.0792-1.69791.2126-1.4124.55640.0343-1.3618-0.21350.091-0.4716-0.388-0.27671.56910.36060.6021-0.3693-0.08251.25170.13690.7447-4.469-31.673129.704
64.46271.1233-0.22233.64640.8456.1244-0.0588-1.4697-0.53080.2801-0.19560.220.5214-0.3840.1710.9042-0.1524-0.05251.94890.11920.5615-31.025-40.551156.757
72.8352.1607-2.95942.759-1.1322.02670.3073-1.5335-0.41430.164-0.6246-0.4805-0.2381.40910.20940.6089-0.3048-0.19471.34540.2240.619339.7923.488131.79
83.2072-0.9231-2.73688.649-2.24898.85480.24530.2086-0.4863-0.2934-0.49950.43480.34391.50370.17610.7736-0.0541-0.13351.1805-0.15830.592315.28-11.513152.607
93.9611-1.89111.53132.3453-2.16822.3972-0.2974-0.13490.10150.13490.42780.0277-0.2432-0.5204-0.18620.91840.0291-0.06371.40420.04520.5407-12.11624.67521.856
103.3592-0.0982-2.2344.6214-0.35826.17080.1820.22010.15360.0435-0.6284-0.4309-1.02330.21440.35581.09210.0826-0.08431.49490.24040.560212.3838.63142.277
114.6979-0.98893.81060.8873-0.63813.5159-0.46660.32290.6265-0.0129-0.119-0.0748-0.917-0.18720.52130.98510.0354-0.17451.55520.06450.722839.6433.57321.46
125.0708-1.9963-1.07627.65420.23124.7601-0.03330.68690.2373-0.4848-0.4052-0.6719-0.60910.11120.48491.0063-0.053-0.08891.15820.14570.550363.672-7.73545.545
132.74330.2278-0.97726.1641-2.0663.68530.0511-0.20950.40760.2139-0.05610.1542-0.7654-0.250.0340.7626-0.0471-0.06760.3578-0.00020.41094.587.87799.179
145.74010.73480.30053.4631.80167.03120.20170.76920.27070.03680.1210.5374-0.5516-1.2929-0.34291.00660.0889-0.03980.88730.27480.7136-5.06619.1771.891
151.56920.2887-0.87599.2675-0.81323.1981-0.3008-0.11680.23130.5985-0.08640.2827-0.4649-0.10160.35131.0895-0.0871-0.11710.4204-0.01550.492952.117-10.953102.023
163.4026-0.92671.00435.06790.04736.8159-0.220.35390.08280.0695-0.03180.2177-0.2183-0.76320.29770.9603-0.1071-0.12060.65710.04540.588543.7161.64373.393
177.58772.7899-1.92843.6923-2.29487.2197-0.24490.0450.1335-0.33760.14810.2128-0.0856-0.75430.04320.4457-0.0962-0.0060.561-0.08720.3961-22.19-32.477118.33
183.49190.33451.80795.6062-0.53817.5831-0.5779-0.57630.54910.17220.78490.1354-1.4262-1.0381-0.18710.76850.02370.00591.5671-0.14390.6276-35.623-27.038146.992
198.42823.9841-1.49822.7795-0.74775.02770.162-0.933-0.2155-0.2006-0.2450.0471-0.015-0.13370.06130.665-0.1357-0.14330.44630.10830.482223.2762.954118.397
203.1159-0.5728-1.4824.45380.45175.5330.2276-0.02340.4889-0.26050.42680.0242-1.87490.6613-0.61591.171-0.425-0.02951.04690.04370.67965.2610.964148.055
213.2504-2.5612-2.30514.24340.1792.6946-0.3796-0.1193-0.3159-0.10350.1508-0.22781.14150.14320.19281.31540.0605-0.20891.6602-0.03160.6285-4.12310.8487.749
222.2628-0.7592-0.23096.2295-0.05296.2440.40730.9219-0.2298-0.612-0.62770.05611.16930.45430.22171.15620.2362-0.1031.6012-0.00410.68645.524-5.66636.623
237.1534-3.5723-2.05452.7010.17341.0237-0.01250.9324-0.3857-0.5253-0.23720.23590.1-0.09440.2340.85610.0905-0.14421.84010.16120.649250.447-9.9629.251
243.74740.24611.12547.8636-1.33963.45310.03360.6696-0.26880.6264-0.34490.21530.804-0.20790.20881.2659-0.1257-0.00481.4261-0.01130.557956.751-21.89739.06
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:127 )H1 - 127
2X-RAY DIFFRACTION2( CHAIN H AND RESID 135:213 )H135 - 213
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:127 )C1 - 127
4X-RAY DIFFRACTION4( CHAIN C AND RESID 135:214 )C135 - 214
5X-RAY DIFFRACTION5( CHAIN G AND RESID 1:126 )G1 - 126
6X-RAY DIFFRACTION6( CHAIN G AND RESID 135:214 )G135 - 214
7X-RAY DIFFRACTION7( CHAIN M AND RESID 1:126 )M1 - 126
8X-RAY DIFFRACTION8( CHAIN M AND RESID 135:214 )M135 - 214
9X-RAY DIFFRACTION9( CHAIN Q AND RESID 1:126 )Q1 - 126
10X-RAY DIFFRACTION10( CHAIN Q AND RESID 136:214 )Q136 - 214
11X-RAY DIFFRACTION11( CHAIN U AND RESID 1:126 )U1 - 126
12X-RAY DIFFRACTION12( CHAIN U AND RESID 135:214 )U135 - 214
13X-RAY DIFFRACTION13( CHAIN L AND RESID 3:113 )L3 - 113
14X-RAY DIFFRACTION14( CHAIN L AND RESID 114:209 )L114 - 209
15X-RAY DIFFRACTION15( CHAIN D AND RESID 3:113 )D3 - 113
16X-RAY DIFFRACTION16( CHAIN D AND RESID 114:209 )D114 - 209
17X-RAY DIFFRACTION17( CHAIN I AND RESID 2:113 )I2 - 113
18X-RAY DIFFRACTION18( CHAIN I AND RESID 114:209 )I114 - 209
19X-RAY DIFFRACTION19( CHAIN N AND RESID 3:113 )N3 - 113
20X-RAY DIFFRACTION20( CHAIN N AND RESID 114:209 )N114 - 209
21X-RAY DIFFRACTION21( CHAIN R AND RESID 3:113 )R3 - 113
22X-RAY DIFFRACTION22( CHAIN R AND RESID 114:209 )R114 - 209
23X-RAY DIFFRACTION23( CHAIN V AND RESID 3:113 )V3 - 113
24X-RAY DIFFRACTION24( CHAIN V AND RESID 114:212 )V114 - 212

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