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- PDB-4ydl: Crystal structure of broadly and potently neutralizing antibody C... -

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Basic information

Entry
Database: PDB / ID: 4ydl
TitleCrystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex with HIV-1 clade AE strain 93TH057gp120
Components
  • Envelope glycoprotein gp160,Envelope glycoprotein gp160
  • HEAVY CHAIN OF ANTIBODY C38-VRC18.02
  • LIGHT CHAIN OF ANTIBODY C38-VRC18.02
KeywordsIMMUNE SYSTEM / Antibody / HIV-1
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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsZhou, T. / Srivatsan, S. / Kwong, P.D.
CitationJournal: Cell / Year: 2015
Title: Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.
Authors: Zhou, T. / Lynch, R.M. / Chen, L. / Acharya, P. / Wu, X. / Doria-Rose, N.A. / Joyce, M.G. / Lingwood, D. / Soto, C. / Bailer, R.T. / Ernandes, M.J. / Kong, R. / Longo, N.S. / Louder, M.K. / ...Authors: Zhou, T. / Lynch, R.M. / Chen, L. / Acharya, P. / Wu, X. / Doria-Rose, N.A. / Joyce, M.G. / Lingwood, D. / Soto, C. / Bailer, R.T. / Ernandes, M.J. / Kong, R. / Longo, N.S. / Louder, M.K. / McKee, K. / O'Dell, S. / Schmidt, S.D. / Tran, L. / Yang, Z. / Druz, A. / Luongo, T.S. / Moquin, S. / Srivatsan, S. / Yang, Y. / Zhang, B. / Zheng, A. / Pancera, M. / Kirys, T. / Georgiev, I.S. / Gindin, T. / Peng, H.P. / Yang, A.S. / Mullikin, J.C. / Gray, M.D. / Stamatatos, L. / Burton, D.R. / Koff, W.C. / Cohen, M.S. / Haynes, B.F. / Casazza, J.P. / Connors, M. / Corti, D. / Lanzavecchia, A. / Sattentau, Q.J. / Weiss, R.A. / West, A.P. / Bjorkman, P.J. / Scheid, J.F. / Nussenzweig, M.C. / Shapiro, L. / Mascola, J.R. / Kwong, P.D.
History
DepositionFeb 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Envelope glycoprotein gp160,Envelope glycoprotein gp160
H: HEAVY CHAIN OF ANTIBODY C38-VRC18.02
L: LIGHT CHAIN OF ANTIBODY C38-VRC18.02
A: Envelope glycoprotein gp160,Envelope glycoprotein gp160
B: HEAVY CHAIN OF ANTIBODY C38-VRC18.02
C: LIGHT CHAIN OF ANTIBODY C38-VRC18.02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,44133
Polymers173,8106
Non-polymers5,63127
Water25,2571402
1
G: Envelope glycoprotein gp160,Envelope glycoprotein gp160
H: HEAVY CHAIN OF ANTIBODY C38-VRC18.02
L: LIGHT CHAIN OF ANTIBODY C38-VRC18.02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,67316
Polymers86,9053
Non-polymers2,76813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Envelope glycoprotein gp160,Envelope glycoprotein gp160
B: HEAVY CHAIN OF ANTIBODY C38-VRC18.02
C: LIGHT CHAIN OF ANTIBODY C38-VRC18.02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,76917
Polymers86,9053
Non-polymers2,86414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.330, 213.089, 68.185
Angle α, β, γ (deg.)90.000, 90.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HBLC

#2: Antibody HEAVY CHAIN OF ANTIBODY C38-VRC18.02


Mass: 24402.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody LIGHT CHAIN OF ANTIBODY C38-VRC18.02


Mass: 23291.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 24 molecules GA

#1: Protein Envelope glycoprotein gp160,Envelope glycoprotein gp160


Mass: 39211.434 Da / Num. of mol.: 2 / Fragment: UNP residues 43-122, 201-303, 325-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK 293 GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q0ED31
#4: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1407 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1402 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9.0% PEG 4000, 4.5% isopropanol, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Number: 607672 / Rmerge(I) obs: 0.063 / Χ2: 1.74 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 175625 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.885010.0441.0853.6
3.884.8810.0431.123.7
3.393.8810.0511.3843.7
3.083.3910.0631.5153.6
2.863.0810.0721.5613.6
2.692.8610.071.4213.5
2.552.6910.0751.3293.5
2.442.5510.0861.3443.5
2.352.4410.0981.3593.5
2.272.3510.1281.8793.4
2.22.2710.1812.6283.3
2.132.210.1521.4673.4
2.082.1310.1911.6823.4
2.032.0810.2391.9793.4
1.982.0310.2581.5943.4
1.941.9810.3261.9013.4
1.91.9410.6364.2253.3
1.861.910.5361.9833.4
1.831.8610.5911.9153.3
1.81.8310.7211.9633.2
ReflectionResolution: 1.8→50 Å / Num. obs: 175625 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 30.25 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.74 / Net I/av σ(I): 17.595 / Net I/σ(I): 13.9 / Num. measured all: 607672
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.833.20.721287061.96398.9
1.83-1.863.30.59187611.91599
1.86-1.93.40.53687631.98398.8
1.9-1.943.30.63686494.22598.2
1.94-1.983.40.32687831.90199
1.98-2.033.40.25888241.59498.9
2.03-2.083.40.23987601.97998.7
2.08-2.133.40.19187071.68299.2
2.13-2.23.40.15287641.46799.3
2.2-2.273.30.18187312.62898.4
2.27-2.353.40.12887571.87998.8
2.35-2.443.50.09887821.35999.1
2.44-2.553.50.08688211.34499
2.55-2.693.50.07587211.32998.9
2.69-2.863.50.0787911.42199.1
2.86-3.083.60.07288361.56199.5
3.08-3.393.60.06388731.51599.9
3.39-3.883.70.05188601.38499.9
3.88-4.883.70.04389061.1299.8
4.88-503.60.04488301.08598.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_1702refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE9

3se9


Resolution: 1.8→35.855 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 8573 5.01 %Random selection
Rwork0.1739 162665 --
obs0.1755 171238 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.72 Å2 / Biso mean: 45.0128 Å2 / Biso min: 18.02 Å2
Refinement stepCycle: final / Resolution: 1.8→35.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12050 0 353 1402 13805
Biso mean--66.72 49.29 -
Num. residues----1557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712721
X-RAY DIFFRACTIONf_angle_d1.06517270
X-RAY DIFFRACTIONf_chiral_restr0.0441974
X-RAY DIFFRACTIONf_plane_restr0.0052208
X-RAY DIFFRACTIONf_dihedral_angle_d12.2774600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.32632820.26775326560898
1.8205-1.84190.27442900.25355458574898
1.8419-1.86430.27763010.25265261556297
1.8643-1.88790.32842780.26825429570798
1.8879-1.91280.38272820.34985134541694
1.9128-1.9390.34882500.31635276552695
1.939-1.96670.24262810.22785381566298
1.9667-1.9960.26722920.21495434572698
1.996-2.02720.24572810.21315420570198
2.0272-2.06040.24943260.21715364569098
2.0604-2.0960.23952730.21515360563399
2.096-2.13410.23332850.19565557584299
2.1341-2.17510.23452600.19475411567199
2.1751-2.21950.25153120.20675446575898
2.2195-2.26780.27612640.2525294555895
2.2678-2.32050.22982800.20265366564698
2.3205-2.37850.21863000.18455474577499
2.3785-2.44280.22582950.19475472576799
2.4428-2.51470.23612670.19015417568499
2.5147-2.59580.23932970.1945417571499
2.5958-2.68860.23533050.19125415572099
2.6886-2.79620.24233070.18955474578199
2.7962-2.92340.2232930.18045450574399
2.9234-3.07740.21683030.175355035806100
3.0774-3.27010.1973040.166454915795100
3.2701-3.52240.18932730.153655615834100
3.5224-3.87650.17892720.146754985770100
3.8765-4.43660.13832850.12955505835100
4.4366-5.58620.16482800.12855585838100
5.5862-35.86190.17812550.15595468572397
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)
13.6109-1.9611-0.44263.81220.16582.3642-0.1756-0.3579-0.24860.45220.20710.23920.4384-0.0163-0.04890.493-0.01280.0640.3260.07560.2955-29.612954.0367-64.8368
22.7304-0.8091-0.69523.8691-0.24541.9152-0.15130.1461-0.3719-0.21130.09580.33120.6053-0.26390.05540.4455-0.12090.03280.28720.04070.3305-32.689451.84-87.4597
32.28450.5168-1.31152.5501-0.14594.9306-0.15940.0098-0.2786-0.20380.1836-0.17720.3130.1108-0.04990.20160.01270.04240.1525-0.00920.2356-15.390272.8313-93.4612
43.80461.5578-0.38894.79650.83593.6861-0.20230.14570.1007-0.34030.1026-0.1925-0.13860.33620.09640.1787-0.02060.01850.26940.01980.14052.705199.6131-111.146
51.44771.3403-0.38146.8583-0.90513.29820.0465-0.08280.0102-0.06190.02330.0486-0.09240.046-0.06050.130.02390.04220.2179-0.00770.1575-22.787792.5819-84.8354
61.514-0.0579-1.3282.05330.85689.15640.00310.33710.0809-0.2557-0.00750.15330.0034-0.2570.01870.1587-0.0488-0.04290.26850.02560.202-10.3993107.3161-115.3066
73.5422-1.83370.6053.60.12432.442-0.1625-0.36180.2470.42970.2066-0.2254-0.3803-0.0036-0.04730.4848-0.0189-0.06020.3317-0.07110.2969-3.16938.9964-30.7075
83.0052-0.76320.83753.7734-0.0831.8732-0.17420.13880.3695-0.22990.1103-0.3557-0.59570.26750.03980.458-0.1183-0.0260.2908-0.04610.3381-0.064941.2582-53.3454
92.31890.54641.27262.35570.1674.8252-0.15490.02160.2935-0.21850.18130.1705-0.3314-0.0985-0.05460.22470.0164-0.04980.14820.00590.2394-17.328920.2004-59.3454
103.90921.34690.27664.5294-1.06563.7625-0.23810.1948-0.0992-0.3390.12990.16060.1304-0.31620.120.1823-0.0281-0.02870.2791-0.01770.1439-35.3024-6.5649-77.0449
111.20481.37920.27246.72990.9233.20790.0426-0.0757-0.0396-0.04210.0208-0.05490.1323-0.0323-0.05160.13410.0259-0.04450.21970.00640.1672-9.94960.4528-50.7153
121.8501-0.05440.37422.2805-0.34193.3612-0.01060.3608-0.0862-0.28740.0003-0.14010.06760.14410.01840.1936-0.03860.03240.2833-0.02580.2036-22.2055-14.2509-81.1923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain G and (resid 44:253 or resid 476:492)G44 - 253
2X-RAY DIFFRACTION1chain G and (resid 44:253 or resid 476:492)G476 - 492
3X-RAY DIFFRACTION2chain G and resid 254:475G254 - 475
4X-RAY DIFFRACTION3chain H and resid 1:113H1 - 113
5X-RAY DIFFRACTION4chain H and resid 114:216H114 - 216
6X-RAY DIFFRACTION5chain L and resid 1:108L1 - 108
7X-RAY DIFFRACTION6chain L and resid 109:214L109 - 214
8X-RAY DIFFRACTION7chain A and (resid 44:253 or resid 476:492)A44 - 253
9X-RAY DIFFRACTION7chain A and (resid 44:253 or resid 476:492)A476 - 492
10X-RAY DIFFRACTION8chain A and resid 254:475A254 - 475
11X-RAY DIFFRACTION9chain B and resid 1:113B1 - 113
12X-RAY DIFFRACTION10chain B and resid 114:216B114 - 216
13X-RAY DIFFRACTION11chain C and resid 1:108C1 - 108
14X-RAY DIFFRACTION12chain C and resid 109:214C109 - 214

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