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- PDB-4xny: Crystal structure of broadly and potently neutralizing antibody V... -

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Basic information

Entry
Database: PDB / ID: 4xny
TitleCrystal structure of broadly and potently neutralizing antibody VRC08C in complex with HIV-1 clade A strain Q842.d12 gp120
Components
  • Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160
  • HEAVY CHAIN OF ANTIBODY VRC08C
  • LIGHT CHAIN OF ANTIBODY VRC08C
KeywordsIMMUNE SYSTEM / Antibody / HIV-1
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / host cell endosome membrane / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / clathrin-dependent endocytosis of virus by host cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / viral protein processing / immune response / 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 / extracellular space / extracellular exosome / extracellular region / membrane / 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 ...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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhou, T. / Srivatsan, S. / Kwong, P.D.
CitationJournal: Cell / Year: 2015
Title: Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.
Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / ...Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / Saunders, K.O. / Soto, C. / Srivatsan, S. / Yang, Y. / Bailer, R.T. / Louder, M.K. / Mullikin, J.C. / Connors, M. / Kwong, P.D. / Mascola, J.R. / Shapiro, L.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 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
Revision 1.4Oct 23, 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
G: Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160
H: HEAVY CHAIN OF ANTIBODY VRC08C
L: LIGHT CHAIN OF ANTIBODY VRC08C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,32514
Polymers87,8923
Non-polymers2,43311
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint20 kcal/mol
Surface area35120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.476, 121.476, 68.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160


Mass: 39667.828 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 43-122, 195-297, 319-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: Q842.d12 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK 293 GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q8JDI3
#2: Antibody HEAVY CHAIN OF ANTIBODY VRC08C


Mass: 25296.432 Da / Num. of mol.: 1
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) / References: UniProt: P01857*PLUS
#3: Antibody LIGHT CHAIN OF ANTIBODY VRC08C


Mass: 22927.490 Da / Num. of mol.: 1
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) / References: UniProt: P01834*PLUS
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 13% PEG 1500, 2% MPD, 0.1M Tris-HCl, pH 8.5

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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: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 44444 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 47.87 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Χ2: 2.23 / Net I/av σ(I): 27.169 / Net I/σ(I): 11.9 / Num. measured all: 168055
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.10.5641.920960.6940.3640.6741.10194.4
2.34-2.383.30.55321750.7190.3480.6551.13797.7
2.38-2.433.60.5221970.7710.3150.611.16399.7
2.43-2.483.80.47322400.8170.280.5511.15499.2
2.48-2.533.90.4322150.8260.2510.4991.28599.8
2.53-2.5940.35922070.880.2080.4151.36199.4
2.59-2.6640.30522280.9070.1770.3531.4799.5
2.66-2.7340.25922000.9360.1510.31.59899.8
2.73-2.8140.23422180.9420.1360.2711.65399.6
2.81-2.93.90.19222460.9580.1130.2231.83699.7
2.9-33.90.16322170.9720.0950.1892.00699.8
3-3.123.90.13322240.9780.0790.1552.19199.5
3.12-3.263.90.11322280.9830.0660.1312.42599.7
3.26-3.443.90.09422280.9870.0560.1092.77499.8
3.44-3.653.90.08122200.990.0480.0943.13399.7
3.65-3.933.80.07722530.9910.0460.0893.70599.7
3.93-4.333.70.06422610.9930.0390.0753.999.8
4.33-4.953.80.05222490.9950.0310.0613.63899.6
4.95-6.243.80.04822490.9960.0290.0563.28399.5
6.24-503.50.04522930.9950.0290.0543.44297.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
PHENIXdev_1702refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XMP

4xmp


Resolution: 2.3→33.691 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 2241 5.05 %
Rwork0.1822 42165 -
obs0.184 44406 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.15 Å2 / Biso mean: 67.9327 Å2 / Biso min: 29.84 Å2
Refinement stepCycle: final / Resolution: 2.3→33.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 308 205 6540
Biso mean--98.12 49.7 -
Num. residues----779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036340
X-RAY DIFFRACTIONf_angle_d0.8338613
X-RAY DIFFRACTIONf_chiral_restr0.052988
X-RAY DIFFRACTIONf_plane_restr0.0031104
X-RAY DIFFRACTIONf_dihedral_angle_d11.9012282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2967-2.34660.34341400.2822360250092
2.3466-2.40120.28821290.28052618274798
2.4012-2.46120.33441410.2772644278599
2.4612-2.52780.27331360.263226502786100
2.5278-2.60210.29991560.24932585274199
2.6021-2.68610.2831510.23722652280399
2.6861-2.7820.25751320.235726342766100
2.782-2.89340.2621290.225126732802100
2.8934-3.0250.25651300.2226652795100
3.025-3.18430.24561420.208526362778100
3.1843-3.38370.2491100.197226882798100
3.3837-3.64460.19291430.183526452788100
3.6446-4.01090.22871400.162926832823100
4.0109-4.590.17531470.143326572804100
4.59-5.77820.15891580.134226832841100
5.7782-33.6950.19211570.15192692284998
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)
16.1048-2.6306-3.87147.30624.11755.3189-0.37760.3096-0.1057-0.36880.63660.15070.0652-0.0247-0.17720.4125-0.1624-0.09540.59340.10880.4321-4.00352.1397-33.2666
22.18740.31430.70046.46591.47452.5647-0.15010.4937-0.2305-0.55570.4917-0.1680.29660.3955-0.37220.476-0.056-0.04460.6490.04370.4652.832942.0893-30.4548
30.84960.40160.38039.0033.18274.86340.18630.08210.40930.2626-0.1492-0.3144-0.40490.3417-0.08690.4097-0.0695-0.05590.54390.20390.5921-1.129165.4953-18.9499
42.983-0.9671-1.40355.14022.30097.19610.00030.6103-0.5572-0.3457-0.02110.16610.9709-0.00520.00390.5056-0.0231-0.08940.516-0.0290.49720.93337.2292-29.1558
57.1888-1.4781-0.42593.8693-0.1871.7931-0.12880.4064-0.5583-0.23990.17660.09620.31270.1695-0.06430.47740.0195-0.11520.371-0.03820.36583.531935.3576-14.4473
64.1548-1.8369-0.17243.38981.43661.5701-0.0475-0.1816-0.15690.27310.11710.0240.2994-0.1261-0.05960.3586-0.0436-0.04430.370.06810.3544-4.063743.6515-5.4595
71.3893-0.0449-1.1179.8198-3.7973.52470.2336-0.5161-0.17950.4297-0.3095-0.27720.1050.2740.03850.3974-0.0344-0.12950.46160.06810.4323-4.064247.9753-0.4691
83.2489-0.8561-0.53174.62930.33021.3661-0.10320.23510.3571-0.08840.1156-0.1365-0.0768-0.0337-0.00330.2929-0.0189-0.04110.33930.04740.3207-2.991155.3599-11.6937
96.65171.4241-4.20015.65292.09026.38660.1932-1.0768-1.12180.66610.3055-0.09930.59360.2634-0.3750.4446-0.0019-0.1470.39810.0150.550811.113236.4171-0.7313
105.00991.70781.37787.70454.22067.75690.16320.5123-0.3702-0.13530.1972-0.43050.42610.202-0.3860.50410.0536-0.03760.59650.03460.49595.19340.8823-27.8802
116.7705-1.1451-3.40914.9023-3.30547.41660.19590.5670.4672-0.2787-0.5717-0.4903-0.7475-0.64660.1750.34720.0953-0.02480.4239-0.06280.591429.360854.64515.2301
125.717-1.77081.18973.5750.89582.33350.1390.15130.0673-0.173-0.12390.21980.0488-0.02570.00160.33630.0691-0.01560.38340.03190.355221.74247.757-1.0965
135.3515-1.7712.41544.1983-1.86014.2132-0.0346-0.36760.1452-0.04750.0718-0.08130.0682-0.2432-0.20790.32870.0402-0.01960.3872-0.05460.419324.422450.82185.4573
144.9549-2.37154.41071.4797-2.26593.79880.37032.95980.010.2277-0.31870.49160.30952.1480.08220.66520.16460.08561.07860.16640.647220.924349.1801-20.0973
154.349-0.60332.36652.05071.19924.68020.0752-0.076-0.01360.09470.0628-0.2336-0.0602-0.0506-0.03720.29820.04770.02930.24910.0270.443238.510744.002912.4507
167.5632-1.49771.40612.49760.27884.2216-0.0812-0.31250.56970.0132-0.0287-0.3812-0.32980.21650.10990.42750.0539-0.09950.4839-0.08980.529152.344346.83825.2436
174.0363-1.86820.47261.5788-0.68833.34730.79480.8373-1.1072-0.3543-0.48730.47630.74520.1659-0.21450.62380.2407-0.1660.5067-0.18340.59234.874427.3128-5.088
182.4798-3.2513-1.88195.08012.77799.65110.95461.94731.066-0.8325-0.5244-0.79120.19430.5033-0.10780.64720.3611-0.04781.06850.05350.379739.235437.3629-11.2451
194.2004-3.80940.08563.12080.21682.67080.59081.3483-0.7821-0.8694-0.61780.31390.37830.29970.04810.64230.2597-0.08020.604-0.13970.471837.394730.3982-6.7446
201.3532-1.3803-1.00712.09740.22724.3114-0.1525-0.32630.21480.28380.1944-0.2644-0.38050.1020.01220.46870.0501-0.0430.5260.01420.46649.914334.019922.5396
217.8748-4.487-4.98554.62032.56994.2244-0.3562-0.1762-0.34490.3822-0.05980.40860.0603-0.5020.34620.41420.0642-0.00450.37190.01210.374146.764629.656623.1787
227.6111.4462-3.05123.53910.02634.17030.07-0.41560.37940.135-0.0097-0.0543-0.3285-0.1999-0.00680.30.0974-0.06010.4273-0.06830.365645.825632.312819.7819
233.5226-1.5265-1.70742.28832.3643.9528-0.5777-0.844-0.07840.58280.2060.2360.4288-0.18310.31950.57930.167-0.00150.66430.01290.39244.666228.931631.6338
244.2673-0.3789-4.13414.90943.72888.42970.1472-1.72280.03950.43610.0579-0.44480.68460.7423-0.46260.82270.3113-0.11990.9169-0.01830.516251.479728.799237.8633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 45 through 76 )G0
2X-RAY DIFFRACTION2chain 'G' and (resid 77 through 115 )G0
3X-RAY DIFFRACTION3chain 'G' and (resid 116 through 215 )G0
4X-RAY DIFFRACTION4chain 'G' and (resid 216 through 258 )G0
5X-RAY DIFFRACTION5chain 'G' and (resid 259 through 283 )G0
6X-RAY DIFFRACTION6chain 'G' and (resid 284 through 385 )G0
7X-RAY DIFFRACTION7chain 'G' and (resid 386 through 425 )G0
8X-RAY DIFFRACTION8chain 'G' and (resid 426 through 456 )G0
9X-RAY DIFFRACTION9chain 'G' and (resid 457 through 474 )G0
10X-RAY DIFFRACTION10chain 'G' and (resid 475 through 492 )G0
11X-RAY DIFFRACTION11chain 'H' and (resid 1 through 17 )H0
12X-RAY DIFFRACTION12chain 'H' and (resid 18 through 72 )H0
13X-RAY DIFFRACTION13chain 'H' and (resid 73 through 93 )H0
14X-RAY DIFFRACTION14chain 'H' and (resid 94 through 100F)H0
15X-RAY DIFFRACTION15chain 'H' and (resid 100G through 135 )H0
16X-RAY DIFFRACTION16chain 'H' and (resid 136 through 215 )H0
17X-RAY DIFFRACTION17chain 'L' and (resid 1 through 38 )L0
18X-RAY DIFFRACTION18chain 'L' and (resid 39 through 61 )L0
19X-RAY DIFFRACTION19chain 'L' and (resid 62 through 101 )L0
20X-RAY DIFFRACTION20chain 'L' and (resid 102 through 128 )L0
21X-RAY DIFFRACTION21chain 'L' and (resid 129 through 150 )L0
22X-RAY DIFFRACTION22chain 'L' and (resid 151 through 174 )L0
23X-RAY DIFFRACTION23chain 'L' and (resid 175 through 204 )L0
24X-RAY DIFFRACTION24chain 'L' and (resid 205 through 214 )L0

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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