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- PDB-5t6l: Crystal structure of 10E8 Fab in complex with the MPER epitope sc... -

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Basic information

Entry
Database: PDB / ID: 5t6l
TitleCrystal structure of 10E8 Fab in complex with the MPER epitope scaffold T117v2
Components
  • (Antibody 10E8 FAB ...) x 2
  • 10E8 EPITOPE SCAFFOLD T117V2
KeywordsIMMUNE SYSTEM / HIV-1 GP41 MPER / 10E8 FAB / LIPID MEMBRANE
Function / homologyMannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIrimia, A. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI084817 United States
Scripps CHAVI-IDUM1 AI100663 United States
CitationJournal: PLoS Pathog. / Year: 2017
Title: Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design.
Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / ...Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / Burton, D.R. / Schief, W.R. / Wilson, I.A.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody 10E8 FAB HEAVY CHAIN
L: Antibody 10E8 FAB LIGHT CHAIN
A: Antibody 10E8 FAB HEAVY CHAIN
B: Antibody 10E8 FAB LIGHT CHAIN
G: 10E8 EPITOPE SCAFFOLD T117V2
I: 10E8 EPITOPE SCAFFOLD T117V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,96424
Polymers134,1606
Non-polymers1,80418
Water7,296405
1
H: Antibody 10E8 FAB HEAVY CHAIN
L: Antibody 10E8 FAB LIGHT CHAIN
I: 10E8 EPITOPE SCAFFOLD T117V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7799
Polymers67,0803
Non-polymers6996
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-34 kcal/mol
Surface area25720 Å2
MethodPISA
2
A: Antibody 10E8 FAB HEAVY CHAIN
B: Antibody 10E8 FAB LIGHT CHAIN
G: 10E8 EPITOPE SCAFFOLD T117V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,18515
Polymers67,0803
Non-polymers1,10512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-39 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.100, 158.970, 99.690
Angle α, β, γ (deg.)90.00, 97.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules GI

#3: Protein 10E8 EPITOPE SCAFFOLD T117V2


Mass: 18643.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 STAR

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Antibody , 2 types, 4 molecules HALB

#1: Antibody Antibody 10E8 FAB HEAVY CHAIN


Mass: 25447.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-15*05 / Plasmid: PHCMV3 / Cell line (production host): HEK 293S / Production host: Homo sapiens (human)
#2: Antibody Antibody 10E8 FAB LIGHT CHAIN


Mass: 22989.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV3-19*01 / Plasmid: PHCMV3 / Cell line (production host): HEK 293S / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 423 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Hepes pH 7.0, 15% PEG 20,000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03314 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03314 Å / Relative weight: 1
ReflectionResolution: 2.096→47.142 Å / Num. obs: 72210 / % possible obs: 97.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.074 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.6 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
XDSVERSION March 30, 2013 BUILT=20130527data reduction
XSCALEVERSION July 4, 2012 BUILT=20130527data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6F, 3LF6

4g6f

3lf6


Resolution: 2.1→47.14 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.54
RfactorNum. reflection% reflection
Rfree0.218 3620 5.02 %
Rwork0.178 --
obs0.18 72183 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8879 0 117 405 9401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089386
X-RAY DIFFRACTIONf_angle_d0.87712822
X-RAY DIFFRACTIONf_dihedral_angle_d12.475530
X-RAY DIFFRACTIONf_chiral_restr0.0581406
X-RAY DIFFRACTIONf_plane_restr0.0061662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0962-2.12380.29841210.29652350X-RAY DIFFRACTION86
2.1238-2.15290.29551380.27662652X-RAY DIFFRACTION97
2.1529-2.18370.34311340.25982637X-RAY DIFFRACTION98
2.1837-2.21620.32411680.25412591X-RAY DIFFRACTION98
2.2162-2.25090.32741210.25582651X-RAY DIFFRACTION98
2.2509-2.28780.26481460.23082694X-RAY DIFFRACTION98
2.2878-2.32720.27721390.22962591X-RAY DIFFRACTION98
2.3272-2.36950.31861390.22072662X-RAY DIFFRACTION98
2.3695-2.41510.31591380.21572708X-RAY DIFFRACTION98
2.4151-2.46440.24041530.20852552X-RAY DIFFRACTION98
2.4644-2.5180.2451220.20592666X-RAY DIFFRACTION98
2.518-2.57660.28251470.1972700X-RAY DIFFRACTION98
2.5766-2.6410.23471260.18682628X-RAY DIFFRACTION98
2.641-2.71240.25411580.18552670X-RAY DIFFRACTION98
2.7124-2.79220.2681280.18082669X-RAY DIFFRACTION99
2.7922-2.88230.22361500.1842639X-RAY DIFFRACTION98
2.8823-2.98530.22251330.18312648X-RAY DIFFRACTION98
2.9853-3.10480.23371340.17862662X-RAY DIFFRACTION98
3.1048-3.24610.21471410.17382636X-RAY DIFFRACTION98
3.2461-3.41720.21091460.16972682X-RAY DIFFRACTION98
3.4172-3.63120.211300.16012594X-RAY DIFFRACTION97
3.6312-3.91140.18551390.14772639X-RAY DIFFRACTION97
3.9114-4.30480.16151420.14012651X-RAY DIFFRACTION97
4.3048-4.92720.13471460.13232630X-RAY DIFFRACTION97
4.9272-6.20550.19921380.16122679X-RAY DIFFRACTION98
6.2055-47.15430.19791430.17292682X-RAY DIFFRACTION97
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)
11.2805-0.76380.34181.7493-0.9331.1623-0.06570.0186-0.0824-0.06060.0518-0.11720.0659-0.00950.01970.20830.00270.05810.1797-0.01250.23451.5062-31.324121.2037
25.5351-0.89120.07524.19570.63885.8154-0.2994-0.74950.89430.68190.02390.34440.2587-0.810.2290.59260.09220.02220.7069-0.01070.736244.5656-34.872958.9962
33.1299-0.2565-0.97032.37520.00852.0216-0.01410.02330.1904-0.0380.01170.0054-0.11220.009-0.00530.1909-0.00030.00260.1530.00110.202938.4371-16.240824.6007
44.8332-1.50992.532.5856-1.78934.1618-0.4961-0.4890.30310.68490.1281-0.8102-0.4070.28670.28970.59770.0378-0.07230.5456-0.08030.803646.3558-19.013654.6459
51.23551.2278-0.62932.7731-1.18152.021-0.16440.0598-0.0955-0.07440.0647-0.14430.110.04030.12050.20510.01280.02850.1866-0.00950.209930.6163-55.290228.3834
64.58060.30840.03942.9338-0.20833.0788-0.1238-0.09450.5866-1.2242-0.18820.3621-1.1728-0.63220.25391.28940.0406-0.01750.6667-0.21020.512626.5984-46.8933-8.4156
72.22110.080.89522.11220.26444.1838-0.14850.2359-0.3246-0.04230.03250.05670.3898-0.32260.1010.312-0.06310.11820.2798-0.04530.341419.6051-71.113122.0936
83.06131.4517-0.1663.89530.00364.03190.0507-0.1833-0.1734-0.79920.1771-0.711-0.7254-0.2423-0.19220.857-0.15440.22040.6077-0.11640.437428.5293-62.7434-11.7157
91.62120.7527-1.31884.8769-2.04965.60490.12990.02860.14850.24450.04460.1116-0.2578-0.2208-0.1340.34780.05040.06370.26740.06790.350820.388-70.326357.6362
100.9976-0.88610.02515.2133-1.26964.37660.06110.1904-0.0824-0.80470.11370.21740.5158-0.57210.04850.4675-0.09050.07190.40830.0740.432347.8944-16.7974-9.2867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'H' AND (RESID 1 THROUGH 113 )
2X-RAY DIFFRACTION2CHAIN 'H' AND (RESID 114 THROUGH 214 )
3X-RAY DIFFRACTION3CHAIN 'L' AND (RESID 2 THROUGH 107 )
4X-RAY DIFFRACTION4CHAIN 'L' AND (RESID 108 THROUGH 211 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 1 THROUGH 113 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 114 THROUGH 214 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 2 THROUGH 107 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 108 THROUGH 211 )
9X-RAY DIFFRACTION9CHAIN 'G' AND ((RESSEQ 7:159))
10X-RAY DIFFRACTION10CHAIN 'I' AND ((RESSEQ 10:161))

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