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

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Basic information

Entry
Database: PDB / ID: 4xmp
TitleCrystal structure of broadly and potently neutralizing antibody VRC08 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 VRC08
  • LIGHT CHAIN OF ANTIBODY VRC08
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 / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling ...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 / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / complement activation, classical pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / 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 / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / extracellular exosome / extracellular region / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / 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: 1.7831 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 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 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_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_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
Revision 2.2Oct 30, 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 VRC08
L: LIGHT CHAIN OF ANTIBODY VRC08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,55016
Polymers87,9363
Non-polymers2,61413
Water11,313628
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.713, 82.496, 163.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody HEAVY CHAIN OF ANTIBODY VRC08


Mass: 25258.582 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 VRC08


Mass: 23009.785 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

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Protein / Sugars , 2 types, 12 molecules G

#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
#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

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Non-polymers , 2 types, 630 molecules

#5: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
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: Feb 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 88301 / % possible obs: 97.9 % / Redundancy: 6 % / Biso Wilson estimate: 25.55 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.043 / Rrim(I) all: 0.105 / Χ2: 1.37 / Net I/av σ(I): 20.167 / Net I/σ(I): 10.3 / Num. measured all: 528269
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
1.78-1.814.20.6022.3239740.7880.3110.6811.08889.9
1.81-1.844.60.55941690.8230.2790.6271.06693.3
1.84-1.884.90.51442990.8810.2480.5731.11596
1.88-1.925.30.48643390.8930.2280.5381.1597.7
1.92-1.965.60.4143870.9240.1870.4521.25698.3
1.96-25.90.35843600.950.1590.3931.25698
2-2.056.20.31743990.9620.1380.3471.32198.1
2.05-2.116.40.28543940.970.1220.311.35298.3
2.11-2.176.50.26244040.9760.1110.2851.4398.8
2.17-2.246.60.23444180.9810.0980.2541.57398.6
2.24-2.326.70.20844220.9830.0870.2261.51398.7
2.32-2.426.70.17744690.9870.0740.1931.55299
2.42-2.536.70.14944270.990.0630.1631.55499.2
2.53-2.666.70.12844770.9910.0540.1391.41399.2
2.66-2.836.60.10344840.9940.0440.1121.41199.1
2.83-3.046.50.09145010.9930.0390.0991.48599.2
3.04-3.356.30.07445080.9950.0320.0811.4699.4
3.35-3.836.20.06945520.9950.030.0751.26599.5
3.83-4.835.80.07345870.9930.0330.081.29999.1
4.83-5050.07547310.9910.0380.0841.40397.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_1702refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE9,4J6R

3se9

4j6r


Resolution: 1.7831→35.499 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 4409 5 %
Rwork0.1646 83719 -
obs0.1664 88128 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 345.73 Å2 / Biso mean: 49.8852 Å2 / Biso min: 15.21 Å2
Refinement stepCycle: final / Resolution: 1.7831→35.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6037 0 329 628 6994
Biso mean--79.29 44.68 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086371
X-RAY DIFFRACTIONf_angle_d1.0858655
X-RAY DIFFRACTIONf_chiral_restr0.0451005
X-RAY DIFFRACTIONf_plane_restr0.0051106
X-RAY DIFFRACTIONf_dihedral_angle_d12.4122292
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 (%)
1.7831-1.80340.30331190.26442280239981
1.8034-1.82460.30051590.25892523268290
1.8246-1.84680.33781400.25152643278394
1.8468-1.87020.27971410.24262687282895
1.8702-1.89480.26021540.22942727288197
1.8948-1.92080.26731520.23042748290097
1.9208-1.94820.22381470.20862785293298
1.9482-1.97730.22921410.20252762290398
1.9773-2.00820.23771310.19782791292298
2.0082-2.04110.23221440.1952805294998
2.0411-2.07630.24151400.19482795293599
2.0763-2.1140.21181460.1792787293398
2.114-2.15470.21921570.179527982955100
2.1547-2.19870.21371540.18182778293298
2.1987-2.24650.21291230.17212836295998
2.2465-2.29870.20611290.177428682997100
2.2987-2.35620.22911590.17022776293599
2.3562-2.41990.20471680.17592795296399
2.4199-2.49110.22771670.1742790295799
2.4911-2.57150.21661400.179228663006100
2.5715-2.66330.21031570.17492806296399
2.6633-2.76990.21961670.17292851301899
2.7699-2.89590.21141520.17522813296599
2.8959-3.04850.1951510.17262848299999
3.0485-3.23940.22161370.16912862299999
3.2394-3.48930.20651590.15812883304299
3.4893-3.84010.18021460.147728993045100
3.8401-4.39490.16581530.126629003053100
4.3949-5.53370.14811300.11622964309499
5.5337-35.50650.16011460.15533053319998
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)
15.78693.36143.6828.76765.15633.6664-0.12160.1407-0.3423-0.3226-0.0740.3325-0.0523-0.47410.19150.27260.04880.03470.4286-0.07250.247957.293394.5724166.1867
23.39411.36510.9064.28761.82443.29610.0626-0.1921-0.14060.0392-0.16930.24520.1785-0.50780.06820.17680.02540.02410.3305-0.0020.161962.870988.7831161.2851
31.67760.27210.25211.94780.38932.764-0.0024-0.2454-0.1110.1693-0.0292-0.06030.18730.11260.00220.16840.03650.00960.19390.02250.155383.908986.8889163.2896
41.94141.31771.00878.60680.21016.4779-0.0483-0.1236-0.2984-0.20730.0210.33720.3162-0.45370.10190.1930.01150.05020.2252-0.04050.15961.845683.5817156.4981
53.69250.6649-1.54271.3356-0.08772.5539-0.07010.0224-0.0209-0.03180.0319-0.0101-0.11970.01280.05210.17140.0182-0.0220.1126-0.02880.122988.933994.9776137.8069
63.90170.91730.85883.6029-0.16654.7394-0.18390.5180.412-0.92940.296-0.0204-0.51830.4441-0.15250.4785-0.12250.05790.26040.00830.3286113.332696.5054108.0343
71.2408-0.1769-1.50710.8954-0.42438.9003-0.14590.3437-0.3663-0.04790.00270.01731.13210.15020.09670.30650.00090.01770.2768-0.14230.351485.828872.4323124.2734
84.21944.5398-3.94244.6977-4.29756.40250.0118-0.04660.06820.02120.02810.39780.005-0.11810.04050.2320.02010.02020.2262-0.07690.25981.845883.3989126.3383
94.2004-1.99221.72398.3272-4.14658.6197-0.10470.5866-0.3303-0.0242-0.05120.18140.1565-0.31570.17230.1524-0.04660.01110.3441-0.14840.311475.697376.6786122.8778
102.97881.36560.28874.14152.84976.1791-0.20030.5918-0.1856-0.17620.1080.20840.08640.19070.03710.13710.015-0.01330.3001-0.09820.225285.06980.1788121.9567
115.4406-2.3004-7.43142.26982.53322.0511-0.1596-0.3570.54850.18710.06690.01570.1041-0.0288-0.01370.22980.0215-0.0240.336-0.05680.254196.987176.1431107.5235
126.71455.87115.08078.76285.84124.3207-0.25490.37570.4256-0.66710.6363-0.6258-0.56180.7045-0.24710.3317-0.13370.11510.5143-0.20010.4694123.349490.7088110.8756
138.43422.52534.84251.54441.63965.57630.262-0.2438-0.29180.14730.0672-0.31980.19220.2671-0.32520.22410.0321-0.00460.2219-0.08230.2672114.869179.5792114.886
142.25062.40681.55463.84112.04562.7446-0.03730.2408-0.1555-0.02410.4299-0.6434-0.01620.4906-0.22090.2201-0.00960.00950.2833-0.09730.3127117.541980.8374110.9929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 45 through 73 )G0
2X-RAY DIFFRACTION2chain 'G' and (resid 74 through 258 )G0
3X-RAY DIFFRACTION3chain 'G' and (resid 259 through 475 )G0
4X-RAY DIFFRACTION4chain 'G' and (resid 476 through 492 )G0
5X-RAY DIFFRACTION5chain 'H' and (resid 2 through 119 )H0
6X-RAY DIFFRACTION6chain 'H' and (resid 120 through 215 )H0
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 29 )L0
8X-RAY DIFFRACTION8chain 'L' and (resid 30 through 48 )L0
9X-RAY DIFFRACTION9chain 'L' and (resid 49 through 75 )L0
10X-RAY DIFFRACTION10chain 'L' and (resid 76 through 102 )L0
11X-RAY DIFFRACTION11chain 'L' and (resid 103 through 113 )L0
12X-RAY DIFFRACTION12chain 'L' and (resid 114 through 128 )L0
13X-RAY DIFFRACTION13chain 'L' and (resid 129 through 163 )L0
14X-RAY DIFFRACTION14chain 'L' and (resid 164 through 214 )L0

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