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- PDB-5te4: Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6... -

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Basic information

Entry
Database: PDB / ID: 5te4
TitleCrystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade G Strain X2088 gp120 Core
Components
  • HIV-1 clade G strain X2088 gp120
  • Heavy chain of antibody N6
  • Light chain of antibody N6
KeywordsIMMUNE SYSTEM / HIV-1 / VRC01-class Antibody / N6 / CD4-binding site / gp120
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / stimulatory C-type lectin receptor signaling pathway / 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 / membrane => GO:0016020 / viral protein processing ...virus-mediated perturbation of host defense response => GO:0019049 / : / stimulatory C-type lectin receptor signaling pathway / 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion 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 / 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
(R,R)-2,3-BUTANEDIOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsZhou, T. / Kwong, P.D.
CitationJournal: Immunity / Year: 2016
Title: Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth.
Authors: Huang, J. / Kang, B.H. / Ishida, E. / Zhou, T. / Griesman, T. / Sheng, Z. / Wu, F. / Doria-Rose, N.A. / Zhang, B. / McKee, K. / O'Dell, S. / Chuang, G.Y. / Druz, A. / Georgiev, I.S. / ...Authors: Huang, J. / Kang, B.H. / Ishida, E. / Zhou, T. / Griesman, T. / Sheng, Z. / Wu, F. / Doria-Rose, N.A. / Zhang, B. / McKee, K. / O'Dell, S. / Chuang, G.Y. / Druz, A. / Georgiev, I.S. / Schramm, C.A. / Zheng, A. / Joyce, M.G. / Asokan, M. / Ransier, A. / Darko, S. / Migueles, S.A. / Bailer, R.T. / Louder, M.K. / Alam, S.M. / Parks, R. / Kelsoe, G. / Von Holle, T. / Haynes, B.F. / Douek, D.C. / Hirsch, V. / Seaman, M.S. / Shapiro, L. / Mascola, J.R. / Kwong, P.D. / Connors, M.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: HIV-1 clade G strain X2088 gp120
H: Heavy chain of antibody N6
L: Light chain of antibody N6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,17325
Polymers87,5413
Non-polymers3,63122
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-24 kcal/mol
Surface area34760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.764, 72.227, 218.123
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 N6


Mass: 24188.283 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): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Light chain of antibody N6


Mass: 23164.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 13 molecules G

#1: Protein HIV-1 clade G strain X2088 gp120


Mass: 40188.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Extended core portion of HIV-1 gp120 / Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: X2088 / Gene: gp120 / Plasmid: pVRC8400 / Cell (production host): 293 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: C6ZIH2*PLUS
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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 , 4 types, 35 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6 % PEG3350, 20% MPD, 0.1 M Immidazole, pH 6.5 and 0.2 M (NH4)2SO4

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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: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 25646 / % possible obs: 87.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 76.54 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.041 / Rrim(I) all: 0.103 / Χ2: 2.104 / Net I/av σ(I): 21.707 / Net I/σ(I): 10.1 / Num. measured all: 137618
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.75-2.82.10.8517410.1410.6030.72750.9
2.8-2.852.40.6888420.5980.4290.66360.10.82
2.85-2.92.70.65810010.5160.4010.70269.40.78
2.9-2.963.20.49710730.7450.2810.8374.30.578
2.96-3.033.60.40910960.8890.2170.71975.40.468
3.03-3.13.90.38611170.840.1970.86577.90.437
3.1-3.174.30.34511690.8560.1780.95680.70.392
3.17-3.264.60.26412110.9560.1260.99185.20.294
3.26-3.364.90.2612780.9520.1231.0886.90.29
3.36-3.465.10.22413430.9730.1041.23693.10.248
3.46-3.595.40.18213910.9860.0821.44196.10.2
3.59-3.735.90.17214420.9880.0741.53398.60.188
3.73-3.96.40.1714520.9910.0711.7131000.184
3.9-4.116.70.14114570.9930.058299.70.153
4.11-4.366.80.1214650.9940.0492.4721000.13
4.36-4.76.70.114650.9950.0412.95399.80.108
4.7-5.176.80.0914970.9960.0373.27799.80.098
5.17-5.926.90.08514840.9950.0353.1891000.092
5.92-7.466.80.07315280.9970.032.9571000.079
7.46-506.20.05415940.9970.0233.33498.20.059

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→40.185 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 1221 4.99 %
Rwork0.2081 23225 -
obs0.2111 24446 89.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.18 Å2 / Biso mean: 101.1528 Å2 / Biso min: 46.05 Å2
Refinement stepCycle: final / Resolution: 2.75→40.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6020 0 222 25 6267
Biso mean--127.61 69.69 -
Num. residues----775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026405
X-RAY DIFFRACTIONf_angle_d0.5598742
X-RAY DIFFRACTIONf_chiral_restr0.0451004
X-RAY DIFFRACTIONf_plane_restr0.0041106
X-RAY DIFFRACTIONf_dihedral_angle_d9.9223774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7502-2.86030.4679880.37941727181561
2.8603-2.99040.38611100.32152102221274
2.9904-3.1480.33851210.30082290241180
3.148-3.34510.38791350.28362553268889
3.3451-3.60330.31441470.23052803295097
3.6033-3.96560.29171500.206228503000100
3.9656-4.53870.21441530.173128983051100
4.5387-5.71570.21411540.172429383092100
5.7157-40.18890.25751630.19523064322799
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)
17.5703-2.72350.07927.25784.14153.77940.42010.5934-0.4953-0.4077-0.6347-0.01880.19270.40330.00251.46170.1504-0.00290.96080.25230.77379.4761-37.514453.3507
24.5805-1.5163-1.54494.1252-1.24652.67390.13840.2714-0.6548-0.2016-0.5046-0.24530.70280.55080.26211.2580.175-0.0570.88460.0450.647611.5132-30.845846.1023
34.37260.4175-0.24684.0529-0.7735.65790.31940.15920.1723-0.1051-0.4893-0.59150.19880.58540.21740.84770.2292-0.05740.78820.14160.580116.6106-10.960444.7335
43.70675.3108-2.45168.8475-1.60053.66750.16860.16441.09240.5223-0.2244-0.1225-0.2872-0.5699-0.18910.9480.2549-0.07220.7810.07970.607611.4419-3.522953.2477
51.68180.25760.28954.0569-0.05150.30970.29090.25030.1321-1.0284-0.539-0.38830.20520.15090.17221.26630.18630.10410.96580.15540.55119.7845-16.40943.6187
68.07716.2458-1.45154.71-0.80396.1746-1.42040.2032-0.27410.53761.4053-0.9966-0.1911-0.9603-0.08910.57460.1107-0.12590.5389-0.0960.5369-13.9542-1.85726.794
74.1573.1509-0.58774.103-1.56153.0664-0.2307-0.7999-0.22191.53910.28990.59590.22-0.13070.00881.04210.0918-0.02660.8484-0.01180.4116-10.349-11.962533.0753
84.46750.16275.57990.01470.25246.91040.28770.2810.0672-0.9994-0.7055-0.27170.14650.56570.27541.32850.29150.03310.6837-0.08310.4227-0.9594-6.272227.5643
94.1250.8411-0.66876.4396-4.25512.7599-0.1458-0.55310.3933-0.4061-0.1128-0.00930.2219-0.23810.19950.98070.0672-0.07250.8388-0.15930.4488-5.5483-3.325634.91
102.2443-1.2888-1.20852.8723.40124.01040.4927-0.10880.2931-1.0812-1.0823-0.60920.47620.30830.51981.09860.2166-0.17870.744-0.03570.5035-5.50630.290824.316
110.9732-0.264-0.1302-0.0499-0.40520.9014-0.1105-0.36750.50120.3538-0.1946-0.38891.3050.00280.13981.41480.1378-0.20160.7436-0.12180.5087-11.341-2.020119.815
123.6375-0.29712.37466.33282.27649.56680.02580.70270.2058-0.45550.0246-0.13170.21570.26210.10490.5460.0298-0.04120.5811-0.07360.5456-23.40428.64620.9219
137.94760.0040.68216.53413.92332.56290.0623-0.36880.2642-0.1966-0.11280.3910.877-0.81740.18480.53670.0716-0.09580.54660.02190.5432-30.549510.13450.6197
142.0733-0.5214-2.07222.64531.86584.7719-0.51160.2557-0.0878-1.6693-0.4532-0.55410.82571.6819-0.44892.27360.75270.05960.6973-0.14960.65262.8654-14.90447.9322
151.5928-0.32250.49796.29852.01294.45510.14450.1952-0.2237-1.501-0.6565-0.09972.5964-0.17480.29382.53130.73640.08660.4618-0.11540.5894-2.6652-18.331611.0983
163.2791-1.47590.59997.1975-1.60572.2531-0.20240.12540.03240.39940.39860.2181.40460.4066-0.08170.98060.1281-0.04850.6627-0.11610.4963-15.8947.0065-6.2512
176.54473.57810.70996.75471.55914.1592-0.14150.3394-0.35120.30320.305-0.24530.73680.0494-0.01270.81390.1332-0.03440.6677-0.09370.4025-10.82127.9232-5.6664
185.2308-2.4588-0.86689.31520.30787.9995-0.10480.08440.9889-0.43990.4579-0.9921-0.5526-0.1992-0.15230.5418-0.0122-0.03510.54550.09220.6648-12.976120.3436-7.4962
197.9656-5.2072-6.24624.63515.16275.8298-0.21571.53620.33211.0615-0.4905-0.277-0.4556-0.90610.65051.15170.1316-0.14820.9070.18520.7333-14.457814.6533-16.463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 45 through 76 )G45 - 76
2X-RAY DIFFRACTION2chain 'G' and (resid 77 through 258 )G77 - 258
3X-RAY DIFFRACTION3chain 'G' and (resid 259 through 385 )G259 - 385
4X-RAY DIFFRACTION4chain 'G' and (resid 386 through 425 )G386 - 425
5X-RAY DIFFRACTION5chain 'G' and (resid 426 through 491 )G426 - 491
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 17 )H1 - 17
7X-RAY DIFFRACTION7chain 'H' and (resid 18 through 33 )H18 - 33
8X-RAY DIFFRACTION8chain 'H' and (resid 34 through 59 )H34 - 59
9X-RAY DIFFRACTION9chain 'H' and (resid 60 through 82 )H60 - 82
10X-RAY DIFFRACTION10chain 'H' and (resid 82A through 95 )H82
11X-RAY DIFFRACTION11chain 'H' and (resid 96 through 124 )H96 - 124
12X-RAY DIFFRACTION12chain 'H' and (resid 125 through 175 )H125 - 175
13X-RAY DIFFRACTION13chain 'H' and (resid 176 through 215 )H176 - 215
14X-RAY DIFFRACTION14chain 'L' and (resid 1 through 38 )L1 - 38
15X-RAY DIFFRACTION15chain 'L' and (resid 39 through 102 )L39 - 102
16X-RAY DIFFRACTION16chain 'L' and (resid 103 through 143 )L103 - 143
17X-RAY DIFFRACTION17chain 'L' and (resid 144 through 174 )L144 - 174
18X-RAY DIFFRACTION18chain 'L' and (resid 175 through 198 )L175 - 198
19X-RAY DIFFRACTION19chain 'L' and (resid 199 through 214 )L199 - 214

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