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- PDB-5u3k: Crystal Structure of DH511.2 Fab in Complex with HIV-1 gp41 MPER ... -

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Basic information

Entry
Database: PDB / ID: 5u3k
TitleCrystal Structure of DH511.2 Fab in Complex with HIV-1 gp41 MPER 662-683 Peptide
Components
  • DH511.2 Fab Heavy Chain
  • DH511.2 Fab Light Chain
  • gp41 MPER peptide
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 / Neutralizing / Antibody / gp41 / MPER / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.637 Å
AuthorsOfek, G. / Wu, L. / Lougheed, C.S. / Williams, L.D. / Nicely, N.I. / Haynes, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5UM1AII00645 United States
CitationJournal: Sci Immunol / Year: 2017
Title: Potent and broad HIV-neutralizing antibodies in memory B cells and plasma.
Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I. ...Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I.S. / Seaman, M.S. / Parks, R.J. / Marshall, D.J. / Anasti, K. / Yang, G. / Nie, X. / Tumba, N.L. / Wiehe, K. / Wagh, K. / Korber, B. / Kepler, T.B. / Munir Alam, S. / Morris, L. / Kamanga, G. / Cohen, M.S. / Bonsignori, M. / Xia, S.M. / Montefiori, D.C. / Kelsoe, G. / Gao, F. / Mascola, J.R. / Moody, M.A. / Saunders, K.O. / Liao, H.X. / Tomaras, G.D. / Georgiou, G. / Haynes, B.F.
History
DepositionDec 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / software
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: DH511.2 Fab Heavy Chain
L: DH511.2 Fab Light Chain
A: DH511.2 Fab Heavy Chain
B: DH511.2 Fab Light Chain
P: gp41 MPER peptide
C: gp41 MPER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6798
Polymers104,6036
Non-polymers762
Water2,630146
1
H: DH511.2 Fab Heavy Chain
L: DH511.2 Fab Light Chain
P: gp41 MPER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3424
Polymers52,3023
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-38 kcal/mol
Surface area21230 Å2
MethodPISA
2
A: DH511.2 Fab Heavy Chain
B: DH511.2 Fab Light Chain
C: gp41 MPER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3374
Polymers52,3023
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-36 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.396, 75.756, 122.630
Angle α, β, γ (deg.)90.00, 94.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-100-

PHE

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Components

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Protein/peptide , 1 types, 2 molecules PC

#3: Protein/peptide gp41 MPER peptide


Mass: 3733.408 Da / Num. of mol.: 2 / Fragment: gp41 656-683 / Source method: obtained synthetically / Details: gp41 MPER 662-683 Peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q73372*PLUS

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Antibody , 2 types, 4 molecules HALB

#1: Antibody DH511.2 Fab Heavy Chain


Mass: 25101.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Heavy Chain / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody DH511.2 Fab Light Chain


Mass: 23466.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Light Chain / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 148 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 1500, 10% Isopropanol, 0.1 M CaCl2, 0.1 M Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→40.762 Å / Num. obs: 28726 / % possible obs: 96.9 % / Redundancy: 1.7 % / Biso Wilson estimate: 42.46 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.106 / Rrim(I) all: 0.152 / Χ2: 1.051 / Net I/σ(I): 6.7 / Num. measured all: 49360
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
2.65-2.741.70.51628320.596197.9
2.74-2.851.70.4470.663198.5
2.85-2.981.70.3670.766198.4
2.98-3.141.70.2730.795198.5
3.14-3.341.70.1960.892198.6
3.34-3.61.70.1440.94198
3.6-3.961.70.110.96197.2
3.96-4.531.70.0760.979196.4
4.53-5.711.70.0610.988194.7
5.71-501.80.050.992190.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.637→40.762 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 1343 4.68 %
Rwork0.2321 --
obs0.2344 28700 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.637→40.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6827 0 2 146 6975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027017
X-RAY DIFFRACTIONf_angle_d0.529560
X-RAY DIFFRACTIONf_dihedral_angle_d10.1814102
X-RAY DIFFRACTIONf_chiral_restr0.0441062
X-RAY DIFFRACTIONf_plane_restr0.0031210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6369-2.73110.37621530.31932676X-RAY DIFFRACTION96
2.7311-2.84040.38191480.3032731X-RAY DIFFRACTION98
2.8404-2.96960.33811440.2922766X-RAY DIFFRACTION98
2.9696-3.12610.31671410.27732784X-RAY DIFFRACTION98
3.1261-3.32190.32551220.26182810X-RAY DIFFRACTION99
3.3219-3.57830.28711290.23652746X-RAY DIFFRACTION98
3.5783-3.93810.24851380.21642761X-RAY DIFFRACTION97
3.9381-4.50730.26451350.18892711X-RAY DIFFRACTION96
4.5073-5.67630.25131050.18442727X-RAY DIFFRACTION95
5.6763-40.76710.23711280.22822645X-RAY DIFFRACTION91
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)
10.6753-0.3053-0.48372.33370.85181.10290.02360.5110.0573-0.2979-0.58160.0654-0.34340.0313-3.97430.3537-0.177-0.23970.99660.28120.4889-26.047919.517535.33
22.8605-0.02230.4471.06830.38540.2353-0.11691.0618-0.3538-0.3291-0.004-0.3224-0.21630.5031-0.50150.2243-0.0384-0.03030.86410.05540.4577-33.843714.6439.2246
35.50960.8422.3981.62881.02362.7294-0.02740.0780.5267-0.5217-0.08880.382-0.676-0.2442-0.00520.2475-0.0629-0.07530.41690.0260.2854-38.828820.861746.5935
45.9160.32382.50884.10321.81751.75560.03391.00530.4039-0.4797-0.3250.4444-0.37310.1172-0.04360.2029-0.0738-0.08490.6370.16530.4507-37.003722.134435.5851
51.82470.4535-0.43440.5713-0.29091.20530.09270.1582-0.36820.0756-0.1336-0.2272-0.3158-0.25590.19530.238-0.0286-0.06510.67020.05180.4478-35.988112.693246.8849
60.56150.24131.06030.52910.59772.03680.33230.59510.0366-0.3564-0.3206-0.3145-0.30730.86971.30960.3637-0.04570.04560.70680.39120.59752.01316.286137.2889
70.9752-0.86990.95761.2642-0.48933.5992-0.49240.25150.60480.05260.4603-0.070.30170.7649-0.08690.32310.0756-0.09030.97630.15480.7161-2.26613.064635.3548
82.6146-0.3656-3.19848.35861.02614.9508-0.11860.8826-0.9971-0.915-0.317-0.13890.3440.5729-0.19170.28360.1961-0.06040.8514-0.1780.7466-0.0942-0.312831.772
91.87980.0103-0.76821.6563-0.63162.7535-0.18820.53040.286-0.1166-0.14920.2199-0.37610.56080.07750.30210.024-0.0590.87460.09550.622-3.851613.940241.9895
101.1876-0.67281.06272.5665-1.34081.1995-0.25732.0344-1.0642-1.0979-0.5778-0.83860.74870.91770.48430.81920.49640.10811.8793-0.12060.949612.2243-2.644131.6765
114.8337-1.99221.41091.0272-0.5580.65330.38241.5197-0.4545-0.5875-0.35010.0970.1310.6794-0.16010.45520.0121-0.00341.40260.15120.80930.451813.522128.1454
122.3625-1.3749-1.55812.68451.46893.73970.52990.5333-0.79270.1709-0.67540.01510.0188-0.30830.02290.2666-0.0806-0.15490.6924-0.00620.7244-24.0612-1.806456.7337
130.087-0.3625-0.01361.56020.0770.55080.251-0.3135-0.020.07820.2211-0.39240.2940.0223-0.11790.2114-0.0369-0.1240.59080.05170.4033-33.46222.535557.1281
144.23910.3547-1.70754.4450.61473.01920.39311.1241-1.4222-0.5561-0.5723-0.27510.26750.54580.33960.32590.0641-0.10820.8694-0.02620.577-33.6708-2.403945.4135
151.72150.92780.94611.2122-0.42351.68270.1422-0.0185-0.64420.07120.16270.03930.05010.0723-0.16130.2073-0.03-0.06130.69790.06250.5431-30.90470.805553.4664
165.59040.42991.72340.4330.1183.0575-0.2275-0.62480.46150.0321-0.06680.013-0.37990.31-0.10090.23460.0203-0.19310.4452-0.10380.8222-9.7371-8.129951.0695
172.84781.6662-0.83884.04680.16371.3405-0.21921.12280.27850.08730.1192-0.4766-0.02540.28010.07710.2690.0058-0.11010.65020.13780.56465.00677.793348.4196
185.42320.92282.52622.1590.32051.58620.02070.04460.25590.1488-0.0945-0.05390.12210.27790.03510.35930.0602-0.03150.623-0.03570.53435.09257.670552.2103
190.4713-0.49380.0850.7337-0.52931.0237-0.13720.15450.21690.1210.324-0.1916-0.32160.34511.15920.2088-0.0347-0.05380.7995-0.10690.4513-0.648939.098816.3748
201.0867-0.4985-0.31912.86380.92072.48030.13980.4589-0.7937-0.1127-0.00650.00740.16930.376-0.03570.2607-0.0016-0.04610.527-0.01440.3814-7.592532.960522.1631
211.7292-0.36460.57940.5273-0.08040.20980.07250.2053-0.4030.1701-0.1345-0.34810.11830.5077-0.5810.255-0.051-0.06240.8332-0.0480.4147-2.830631.506614.9036
221.3749-0.5824-0.15520.54290.532.86320.093-0.2390.13840.09380.1523-0.11420.073-0.6471-0.07620.2219-0.0509-0.06440.6003-0.01960.3519-10.337141.29333.5855
231.4583-0.7333-0.21661.2398-0.35710.24560.37550.20460.1735-0.4393-0.1555-0.1021-0.322-0.67990.09830.33470.0851-0.03520.54220.07050.3127-16.230642.13851.7665
243.2216-1.0511-0.67240.9055-0.80423.26560.6010.58750.2111-0.2702-0.35110.0595-0.8648-0.6113-0.19270.48940.13240.02850.53960.03160.3201-20.209147.2239-7.057
251.063-0.13661.64571.9823-1.34523.20740.43710.23230.6453-0.3181-0.222-0.3723-0.9723-0.53060.40830.48420.35240.08750.81630.04250.3821-14.62147.9717-14.531
262.15760.5775-0.79720.43690.43633.30750.1150.4374-0.2211-0.36470.14810.7782-0.5476-1.2049-0.05480.30580.0981-0.02820.89880.01930.4128-29.149948.891222.1133
273.0056-0.5823-1.01880.9417-0.66585.46170.1908-0.0596-0.05240.1128-0.00890.2106-0.8228-0.8974-0.09310.33810.0427-0.02870.4672-0.06730.3574-20.803349.109928.4437
281.9271-0.4663-0.25163.4473-1.19274.16540.01010.41340.18810.36770.26780.6068-1.3291-0.11320.04910.64910.0035-0.03150.45610.02580.3073-21.946253.595320.6168
291.4697-0.408-1.02341.78180.52111.29250.2931-0.4506-0.22730.5262-0.28390.4851-0.2693-0.3930.10380.3792-0.08690.03120.4356-0.00640.4201-18.788137.064728.1652
301.844-0.8083-0.19821.3192-0.6392.3741-0.12870.183-0.00180.17830.1545-0.27730.2377-0.4167-0.17010.25720.1179-0.09640.4850.01080.323-32.814458.29248.3303
311.439-0.53650.00233.42091.59291.06330.22220.811-0.2382-0.6576-0.01490.02-0.29830.2190.10310.44910.2338-0.12290.7238-0.0340.5133-32.818848.6004-8.5015
324.12922.36883.58271.42731.80363.9320.81470.0683-1.4689-0.23730.05821.03690.30450.0077-0.24160.59260.0916-0.29910.5072-0.06310.9564-39.334940.3313-6.4185
331.7493-1.1088-0.47471.70811.82812.4491-0.0033-0.0934-0.42390.4173-0.3768-0.43220.0611.0608-0.27540.2741-0.004-0.0970.69720.0070.5419-26.612156.83763.5792
341.55570.44290.81341.127-0.12460.54710.3790.7146-0.8967-0.5064-0.49380.22140.02890.1744-1.32160.5750.1966-0.37080.7148-0.25610.808-38.768743.1511-10.8417
351.9918-1.2086-1.47313.74321.40362.24820.2470.0811-0.8375-0.1971-0.94781.08010.2940.0403-0.30130.382-0.0055-0.16210.9442-0.05020.6869-43.794453.6565-5.1916
360.83730.38820.47320.18380.21540.268-0.34860.23460.4643-0.74420.43580.4261-0.02570.1058-0.28850.7423-0.113-0.28270.61930.09170.4449-54.819213.656637.1862
370.56440.3295-0.09360.3504-0.11190.03580.01380.00040.36420.08620.17050.2734-0.1359-0.01530.11750.18610.08550.01880.909-0.04680.4921-56.217111.775851.3649
380.94622.04070.12568.82762.67531.3218-0.75490.4513-0.6192-0.53820.3272-1.1128-1.03230.89470.12140.3436-0.0071-0.08160.6552-0.04690.40525.984642.085637.5123
394.9580.2278-0.67981.8166-0.63277.8916-0.0531-0.3467-0.8716-0.35460.17150.60430.8711-0.7853-0.10160.36210.0096-0.16970.63580.09050.5453-3.852837.58444.9814
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 45 )
3X-RAY DIFFRACTION3chain 'H' and (resid 46 through 66 )
4X-RAY DIFFRACTION4chain 'H' and (resid 67 through 82 )
5X-RAY DIFFRACTION5chain 'H' and (resid 83 through 111 )
6X-RAY DIFFRACTION6chain 'H' and (resid 112 through 137 )
7X-RAY DIFFRACTION7chain 'H' and (resid 138 through 154 )
8X-RAY DIFFRACTION8chain 'H' and (resid 155 through 165 )
9X-RAY DIFFRACTION9chain 'H' and (resid 166 through 182 )
10X-RAY DIFFRACTION10chain 'H' and (resid 183 through 194 )
11X-RAY DIFFRACTION11chain 'H' and (resid 195 through 212 )
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 18 )
13X-RAY DIFFRACTION13chain 'L' and (resid 19 through 38 )
14X-RAY DIFFRACTION14chain 'L' and (resid 39 through 61 )
15X-RAY DIFFRACTION15chain 'L' and (resid 62 through 102 )
16X-RAY DIFFRACTION16chain 'L' and (resid 103 through 113 )
17X-RAY DIFFRACTION17chain 'L' and (resid 114 through 150 )
18X-RAY DIFFRACTION18chain 'L' and (resid 151 through 212 )
19X-RAY DIFFRACTION19chain 'A' and (resid 1 through 33 )
20X-RAY DIFFRACTION20chain 'A' and (resid 34 through 72 )
21X-RAY DIFFRACTION21chain 'A' and (resid 73 through 87 )
22X-RAY DIFFRACTION22chain 'A' and (resid 88 through 100)
23X-RAY DIFFRACTION23chain 'A' and (resid 101 through 145 )
24X-RAY DIFFRACTION24chain 'A' and (resid 146 through 185 )
25X-RAY DIFFRACTION25chain 'A' and (resid 186 through 213 )
26X-RAY DIFFRACTION26chain 'B' and (resid 1 through 18 )
27X-RAY DIFFRACTION27chain 'B' and (resid 19 through 75 )
28X-RAY DIFFRACTION28chain 'B' and (resid 76 through 90 )
29X-RAY DIFFRACTION29chain 'B' and (resid 91 through 102 )
30X-RAY DIFFRACTION30chain 'B' and (resid 103 through 113 )
31X-RAY DIFFRACTION31chain 'B' and (resid 114 through 144 )
32X-RAY DIFFRACTION32chain 'B' and (resid 145 through 163 )
33X-RAY DIFFRACTION33chain 'B' and (resid 164 through 174 )
34X-RAY DIFFRACTION34chain 'B' and (resid 175 through 197 )
35X-RAY DIFFRACTION35chain 'B' and (resid 198 through 209 )
36X-RAY DIFFRACTION36chain 'P' and (resid 666 through 671 )
37X-RAY DIFFRACTION37chain 'P' and (resid 672 through 685 )
38X-RAY DIFFRACTION38chain 'C' and (resid 667 through 671 )
39X-RAY DIFFRACTION39chain 'C' and (resid 672 through 685 )

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