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- PDB-4u6g: Crystal structure of 10E8 Fab in complex with a hydrocarbon-stapl... -

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Basic information

Entry
Database: PDB / ID: 4u6g
TitleCrystal structure of 10E8 Fab in complex with a hydrocarbon-stapled HIV-1 gp41 MPER peptide
Components
  • 10E8 Fab Heavy Chain
  • 10E8 Fab Light Chain
  • SAH-MPER(662-683KKK)(B,q)
KeywordsIMMUNE SYSTEM / 10E8 Antibody / HIV-1 / hydrocarbon-staple / gp41 MPER
Function / homology
Function and homology information


membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.2012 Å
AuthorsOfek, G. / Bird, G.H. / Walensky, L.D. / Kwong, P.D.
CitationJournal: To be published
Title: Structural Fidelity and Neutralizing Antibody Binding Capacity of Hydrocarbon-Stapled HIV-1 Antigens
Authors: Bird, G.H. / Irimia, A. / Ofek, G. / Kwong, P.D. / Wilson, I.A. / Walensky, L.D.
History
DepositionJul 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Dec 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 10E8 Fab Heavy Chain
L: 10E8 Fab Light Chain
A: 10E8 Fab Heavy Chain
B: 10E8 Fab Light Chain
P: SAH-MPER(662-683KKK)(B,q)
C: SAH-MPER(662-683KKK)(B,q)


Theoretical massNumber of molelcules
Total (without water)101,2576
Polymers101,2576
Non-polymers00
Water0
1
H: 10E8 Fab Heavy Chain
L: 10E8 Fab Light Chain
P: SAH-MPER(662-683KKK)(B,q)


Theoretical massNumber of molelcules
Total (without water)50,6293
Polymers50,6293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-33 kcal/mol
Surface area22040 Å2
MethodPISA
2
A: 10E8 Fab Heavy Chain
B: 10E8 Fab Light Chain
C: SAH-MPER(662-683KKK)(B,q)


Theoretical massNumber of molelcules
Total (without water)50,6293
Polymers50,6293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-33 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.562, 126.317, 129.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: 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) / Plasmid: pVRC8400 / Cell (production host): Embryonic Kidney / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#2: 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) / Plasmid: pVRC8400 / Cell (production host): Embryonic Kidney / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#3: Protein/peptide SAH-MPER(662-683KKK)(B,q)


Mass: 2191.614 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: I3VHW6*PLUS

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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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% Isopropanol, 7.5% PEG 8000, 0.1 M Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2013
RadiationMonochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.15→50 Å / Num. obs: 8148 / % possible obs: 95.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 75.75 Å2 / Rmerge(I) obs: 0.302 / Χ2: 1.058 / Net I/av σ(I): 5.615 / Net I/σ(I): 3.1 / Num. measured all: 52206
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
4.15-4.255.10.5644681.0983.3
4.25-4.355.40.5814671.09386
4.35-4.475.60.4654851.07489
4.47-4.65.70.4235051.01690
4.6-4.755.90.4565161.0891.3
4.75-4.9260.4625351.04494.5
4.92-5.126.10.3945401.08496.3
5.12-5.356.10.4545471.08798
5.35-5.636.40.4485661.07698.6
5.63-5.986.70.4865481.09699.5
5.98-6.447.10.4425801.067100
6.44-7.097.60.385781.031100
7.09-8.117.60.2265821.032100
8.11-10.217.40.1275951.056100
10.21-506.60.103636198.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 4.2012→40.053 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 383 4.73 %
Rwork0.2254 --
obs0.2282 8091 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2012→40.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7020 0 0 0 7020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037215
X-RAY DIFFRACTIONf_angle_d0.649818
X-RAY DIFFRACTIONf_dihedral_angle_d8.4792560
X-RAY DIFFRACTIONf_chiral_restr0.0271071
X-RAY DIFFRACTIONf_plane_restr0.0031254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2012-4.80830.2961260.21282232X-RAY DIFFRACTION84
4.8083-6.05460.27711240.23382631X-RAY DIFFRACTION96
6.0546-40.05510.27361330.22742845X-RAY DIFFRACTION100
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)
12.0734-0.2931.30432.2731-1.6352.02340.0470.09421.35261.02140.2399-1.16640.00860.8952-0.21460.604-0.0984-0.00940.8354-0.18070.914314.1465-9.134522.3605
22.81411.14170.0213.45540.32011.87330.31150.0832-0.0780.58390.2592-0.46310.29060.3243-0.5150.84510.0891-0.04311.09480.07480.679210.2939-14.775330.3212
31.4186-0.40450.54420.603-0.83374.68110.1113-0.21210.4819-0.12960.2864-0.0060.28450.18-0.37590.6442-0.03880.0020.5141-0.12950.84244.1774-11.77988.2146
44.5152-2.33222.0043.1045-0.01682.4166-0.2111-0.67911.0889-0.28140.33550.29240.0623-0.2667-0.02880.7919-0.17160.11730.96260.03511.23287.1351-5.3309-9.6513
52.48860.42743.05433.8271-4.199.6080.01340.26720.1374-0.49640.0607-0.12671.00130.22570.04730.8020.05310.06360.67830.05831.0544-14.2047-21.09521.8909
62.19-1.02360.19135.13160.24243.8659-0.3399-0.19620.12210.27440.5598-0.2052-0.4668-0.2771-0.24430.77330.0510.06340.73680.0160.8161-10.6676-14.049827.7992
70.06240.07390.2931.38520.68392.36310.0316-0.1747-0.2002-0.1643-0.2627-0.09560.3348-0.0780.26020.73050.1133-0.02860.50510.1280.7974-4.3879-16.1576-2.6369
82.601-0.1881-0.58842.86950.77754.52830.13180.5908-0.0295-0.1272-0.29180.1509-0.0728-0.05120.06420.64030.1517-0.01431.09310.07891.1004-3.5382-20.9447-8.6996
91.14520.15111.29390.99380.61052.0504-0.06460.14540.0475-0.3286-0.005-0.1805-0.50230.0164-0.02491.3722-0.2034-0.01771.12410.08030.99865.271715.509612.9097
104.85020.7468-2.41182.0467-0.00344.86550.1438-0.2841-0.76440.0996-0.0167-0.04850.17410.0333-0.08590.7609-0.0122-0.10870.73470.00230.83114.09626.721451.894
114.87835.1866-3.01845.5437-3.24412.7591.62440.18271.07050.5676-1.73420.662-0.4019-0.9706-0.10611.07120.18510.16050.9877-0.04581.0003-19.366518.272824.5615
122.84770.2103-1.73983.6594-2.2293.66670.0413-0.14020.3622-0.34840.03110.115-1.6632-0.41750.40531.45570.0252-0.21491.18940.0110.7772-12.690317.677915.7004
132.5876-2.2472-0.22453.3148-1.14372.6721-0.2613-0.05610.3084-1.26210.2975-0.6256-0.5828-0.8577-0.16281.2689-0.1968-0.07321.07270.15890.884-19.029413.660211.7665
141.68750.93590.51041.60980.49930.1326-0.1095-0.26670.27360.00330.0645-0.2158-0.2223-0.09350.16931.3764-0.0079-0.25080.82640.06841.4646-11.147417.546116.7346
150.8495-0.69060.08660.79720.29091.0417-0.3618-0.3287-0.6268-0.2961-0.34710.4159-0.7180.59260.37510.9545-0.08320.07490.7685-0.31311.0067-15.594913.860930.434
164.22340.21432.32042.49990.09012.9881-0.1951-0.3233-0.02260.20170.291-0.55240.0683-0.1387-0.00890.81980.1151-0.05940.7666-0.11790.8346-5.771919.637551.9425
171.8935-1.60821.65652.4541-0.40216.37170.84130.8530.06841.1253-0.52990.52070.59211.0374-0.21830.96690.07960.12390.45650.0590.8468-2.1187-22.570850.4878
185.126.05910.54828.264-2.51469.30550.7331-0.47020.5060.20690.39410.05621.2029-0.3804-0.69131.2274-0.0553-0.09340.9450.2361.14590.155620.6067-6.5498
191.1296-0.0986-0.11322.64250.43923.30030.8207-0.3902-0.20570.64010.6613-1.50320.74640.8601-0.37681.3651-0.2898-0.3374-0.3335-1.18141.4566-10.645326.9207-10.0215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 98 )
3X-RAY DIFFRACTION3chain 'H' and (resid 99 through 157 )
4X-RAY DIFFRACTION4chain 'H' and (resid 158 through 214 )
5X-RAY DIFFRACTION5chain 'L' and (resid 2 through 29 )
6X-RAY DIFFRACTION6chain 'L' and (resid 30 through 95C)
7X-RAY DIFFRACTION7chain 'L' and (resid 96 through 151 )
8X-RAY DIFFRACTION8chain 'L' and (resid 152 through 211 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 113 )
10X-RAY DIFFRACTION10chain 'A' and (resid 114 through 214 )
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 18 )
12X-RAY DIFFRACTION12chain 'B' and (resid 19 through 48 )
13X-RAY DIFFRACTION13chain 'B' and (resid 49 through 75 )
14X-RAY DIFFRACTION14chain 'B' and (resid 76 through 95C)
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 114 )
16X-RAY DIFFRACTION16chain 'B' and (resid 115 through 211 )
17X-RAY DIFFRACTION17chain 'P' and (resid 668 through 684 )
18X-RAY DIFFRACTION18chain 'C' and (resid 668 through 676 )
19X-RAY DIFFRACTION19chain 'C' and (resid 677 through 684 )

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