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- PDB-4rx4: Crystal structure of VH1-46 germline-derived CD4-binding site-dir... -

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Basic information

Entry
Database: PDB / ID: 4rx4
TitleCrystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC134 in complex with HIV-1 clade A Q842.d12 gp120
Components
  • 8ANC134 Heavy chain
  • 8ANC134 Light Chain
  • HIV-1 Clade A Q842.d12 gp120
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 attachment protein / Broadly neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM 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 / 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 / Resolution: 3.45 Å
AuthorsZhou, T. / Acharya, P. / Moquin, S. / Kwong, P.D.
CitationJournal: Cell(Cambridge,Mass.) / 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
DepositionDec 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Derived calculations
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: HIV-1 Clade A Q842.d12 gp120
H: 8ANC134 Heavy chain
L: 8ANC134 Light Chain
E: HIV-1 Clade A Q842.d12 gp120
A: 8ANC134 Heavy chain
D: 8ANC134 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,98134
Polymers175,0856
Non-polymers3,89628
Water00
1
G: HIV-1 Clade A Q842.d12 gp120
H: 8ANC134 Heavy chain
L: 8ANC134 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,69419
Polymers87,5433
Non-polymers2,15216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-41 kcal/mol
Surface area31930 Å2
2
E: HIV-1 Clade A Q842.d12 gp120
A: 8ANC134 Heavy chain
D: 8ANC134 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,28715
Polymers87,5433
Non-polymers1,74412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-63 kcal/mol
Surface area19930 Å2
Unit cell
Length a, b, c (Å)220.353, 220.353, 118.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Antibody , 2 types, 4 molecules HALD

#2: Antibody 8ANC134 Heavy chain


Mass: 24449.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 8ANC134 heavy chain / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody 8ANC134 Light Chain


Mass: 23425.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 8ANC134 light chain / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 13 molecules GE

#1: Protein HIV-1 Clade A Q842.d12 gp120


Mass: 39667.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: Clade A Q842.d12 / Gene: gp120 / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q8JDI3*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: 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 , 2 types, 17 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2

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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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 8% w/v PEG 8000, 0.2 M sodium acetate and 0.1 m sodium Cacodylate, pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→26.896 Å / Num. obs: 28017 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.103 / Rsym value: 0.061 / Net I/σ(I): 16.8
Reflection shellResolution: 3.45→3.51 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2 / Rsym value: 0.622 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→26.9 Å / SU ML: 0.52 / σ(F): 1.97 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1406 5.02 %
Rwork0.208 --
obs0.21 28008 99.7 %
all-28017 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11741 0 234 0 11975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812253
X-RAY DIFFRACTIONf_angle_d1.49916633
X-RAY DIFFRACTIONf_dihedral_angle_d13.1454441
X-RAY DIFFRACTIONf_chiral_restr0.0561891
X-RAY DIFFRACTIONf_plane_restr0.0072127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.454-3.57690.36311190.28412679X-RAY DIFFRACTION99
3.5769-3.71970.32981430.27072653X-RAY DIFFRACTION100
3.7197-3.88860.32071300.2572663X-RAY DIFFRACTION100
3.8886-4.09290.28741220.24162694X-RAY DIFFRACTION100
4.0929-4.34830.28511400.19982669X-RAY DIFFRACTION100
4.3483-4.68250.22711510.18312669X-RAY DIFFRACTION100
4.6825-5.15070.19961580.17462651X-RAY DIFFRACTION100
5.1507-5.88920.26831440.20662645X-RAY DIFFRACTION100
5.8892-7.39410.29771530.23742654X-RAY DIFFRACTION100
7.3941-26.89630.19541460.17422625X-RAY DIFFRACTION99
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)
12.896-1.0586-1.59893.9071.15742.471-0.0870.1715-0.0412-0.10240.1063-0.0484-0.57130.0873-0.02190.6356-0.0320.00280.64740.01310.75724.789515.789337.3256
22.408-0.0987-0.63543.06380.23655.6182-0.0730.0358-0.1293-0.53710.0678-0.8498-0.15050.5216-0.00910.6113-0.06750.05550.6582-0.02330.881437.81475.182628.5445
35.2652.2055-0.14914.3049-2.44065.0156-1.03550.1639-0.5473-0.98151.0785-0.26470.37770.8865-0.0730.75780.0828-0.12590.9581-0.18860.581225.7223-27.201336.0905
44.05770.6271-0.56884.49071.9293.267-0.11370.1747-0.00330.03010.28640.423-0.11610.0253-0.20260.47920.06890.04230.7369-0.00170.574726.3877-16.146141.5495
52.8042-0.7765-0.02289.0586-0.89994.22910.04361.02230.862-0.4394-0.2833-0.91770.19460.7246-0.16840.67430.1438-0.02481.12490.09150.795735.1684-13.897436.5964
61.73262.1740.83594.234-0.56944.2874-0.00130.03120.4519-0.07180.0291-0.16860.36760.1895-0.09280.56270.08680.0160.6875-0.02810.608726.7246-16.75841.6974
73.3912-0.1474-1.22218.6252-5.65396.1949-0.1372-0.1058-2.4219-0.9959-0.77051.42611.5518-0.15240.82211.00010.17590.21120.7006-0.02361.733228.3671-51.262250.9536
83.1571-3.67790.06656.8234-0.95245.71610.0403-0.3234-2.0770.3487-0.00421.11170.5511-1.115-0.13830.7505-0.09850.0060.64130.15871.538321.5318-52.073854.8629
93.74980.44290.98736.70280.00513.6251-0.1864-0.6166-0.05961.08120.086-0.74340.03520.08340.07510.83570.1931-0.09940.801-0.12720.706231.0101-16.380364.1045
102.34940.5182-3.22126.2007-5.90049.41770.14740.3980.58892.27551.1050.5026-1.3718-2.0999-1.07420.55750.141-0.06821.1071-0.24460.984219.7257-13.317758.7474
113.3238-0.2222-0.40135.31420.06793.0747-0.1703-0.4319-0.48660.9004-0.02610.2920.13510.22840.17420.55340.10720.00170.636-0.03520.593629.3392-27.571762.2875
126.1789-1.5564-1.66274.9526-0.89093.70190.4928-0.4587-0.4440.3917-0.3931-0.45820.19160.1526-0.07880.94410.1046-0.07440.66210.21950.868434.0582-42.638863.6043
134.7201-2.7639-0.27695.81771.53645.87740.2469-0.4055-1.17180.32690.2083-0.49540.82510.8287-0.21590.9330.1437-0.04620.72930.30861.315641.615-51.915963.4583
146.96291.00061.66156.932-0.19797.5710.0523-0.36380.5707-0.15091.1333-0.04530.5809-2.2177-0.65741.2904-0.17490.09970.6155-0.24630.9594.9813-26.4276108.9888
159.28650.3999-2.61632.404-0.50966.388-0.4244-0.8981-0.7653-0.1411-0.1587-0.33921.19980.07940.6091.16910.13320.04760.82970.15071.02138.8897-30.0834104.6114
162.29191.57080.84712.17070.47482.0242-0.6144-1.04890.2247-0.5266-0.54311.4112-0.29081.10961.27020.9721-0.0378-0.0711.015-0.05681.129611.033-17.1999112.304
171.96220.88431.46713.00730.96863.4182-0.1275-0.3660.62510.6144-0.3592-0.38310.3193-0.30150.46971.209-0.2094-0.05570.9835-0.05051.155910.0673-18.7977120.6375
184.08-0.5540.86741.78920.47773.36350.10420.0365-0.2870.35490.0466-0.72110.94190.4928-0.18081.09780.1578-0.08460.6576-0.030.95328.8653-27.7803112.9937
192.95661.81272.13724.06680.10534.7539-0.0663-0.3361-0.15110.640.0195-0.48140.19820.03830.16890.89670.1750.01750.69910.010.796124.3275-20.5601116.2939
209.90362.7878-2.11166.3253-1.53661.31890.5902-0.70550.37891.0078-0.67210.01190.2632-0.11590.1560.857-0.0526-0.06971.0167-0.06940.760233.95518.5105110.0133
213.249-0.66351.60134.6951-0.35344.4806-0.2728-0.6082-0.1962-0.40110.44690.15230.58960.2296-0.12820.5726-0.0475-0.12780.935-0.05190.741229.77970.0107102.4943
226.56372.58853.32037.361-4.89269.3510.53750.5281-1.42880.8465-0.28840.2471-0.19150.5696-0.17280.67650.05460.0860.9286-0.05520.909337.1614-5.4103107.7233
231.5395-0.2584-1.24754.121-0.14051.2744-0.04460.0178-0.67110.38450.0179-0.49210.10170.462-0.00470.6631-0.1776-0.02361.01860.03430.714233.94594.0915104.4075
245.79531.88310.49162.93210.25240.0252-0.27-0.5208-0.15840.4368-0.24780.49970.0361.90520.30650.4371-0.4289-0.02291.2724-0.42451.238653.014934.919686.3619
255.94530.91542.28495.8773-1.98833.7606-0.27770.34810.7922-0.45370.50980.26130.0913-0.7623-0.25240.6193-0.26170.10051.1040.03660.939644.819932.059489.4323
267.8674.97413.37458.6992-1.0533.0636-0.94081.35490.8374-0.75651.12571.20960.4828-1.2768-0.25720.5605-0.250.06090.8302-0.08851.137748.494839.176594.7176
272.925-0.71870.96634.7772-1.41332.6712-0.69420.8885-0.4003-0.41530.4841-0.84090.14450.20590.29840.9527-0.35130.15751.3238-0.40480.997234.6117-1.974181.8038
287.5405-3.33911.34835.0036-3.84936.6516-0.44720.3534-0.2123-0.83831.09390.89310.2733-1.0786-0.62110.7639-0.2783-0.11591.50320.08280.905223.00471.342887.2151
294.39581.92-0.26743.56930.40472.4128-0.961.0855-0.094-1.43390.9116-0.55140.04540.00610.01030.7029-0.32270.00551.1623-0.16250.5340.169410.995183.327
307.17451.6111-0.01773.9467-0.79853.5203-0.05340.1174-0.2836-0.51290.0049-1.08830.6057-0.18570.00360.836-0.31850.24070.9549-0.07980.977855.279720.893881.4086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 45 through 283 )
2X-RAY DIFFRACTION2chain 'G' and (resid 284 through 492 )
3X-RAY DIFFRACTION3chain 'H' and (resid 2 through 17 )
4X-RAY DIFFRACTION4chain 'H' and (resid 18 through 51 )
5X-RAY DIFFRACTION5chain 'H' and (resid 52 through 72 )
6X-RAY DIFFRACTION6chain 'H' and (resid 73 through 109 )
7X-RAY DIFFRACTION7chain 'H' and (resid 110 through 145 )
8X-RAY DIFFRACTION8chain 'H' and (resid 146 through 213 )
9X-RAY DIFFRACTION9chain 'L' and (resid 2 through 38 )
10X-RAY DIFFRACTION10chain 'L' and (resid 39 through 61 )
11X-RAY DIFFRACTION11chain 'L' and (resid 62 through 128 )
12X-RAY DIFFRACTION12chain 'L' and (resid 129 through 174 )
13X-RAY DIFFRACTION13chain 'L' and (resid 175 through 214 )
14X-RAY DIFFRACTION14chain 'E' and (resid 44 through 64 )
15X-RAY DIFFRACTION15chain 'E' and (resid 65 through 98 )
16X-RAY DIFFRACTION16chain 'E' and (resid 99 through 115 )
17X-RAY DIFFRACTION17chain 'E' and (resid 116 through 222 )
18X-RAY DIFFRACTION18chain 'E' and (resid 223 through 413 )
19X-RAY DIFFRACTION19chain 'E' and (resid 414 through 492 )
20X-RAY DIFFRACTION20chain 'A' and (resid 2 through 25 )
21X-RAY DIFFRACTION21chain 'A' and (resid 26 through 45 )
22X-RAY DIFFRACTION22chain 'A' and (resid 46 through 72 )
23X-RAY DIFFRACTION23chain 'A' and (resid 73 through 119 )
24X-RAY DIFFRACTION24chain 'A' and (resid 120 through 135 )
25X-RAY DIFFRACTION25chain 'A' and (resid 136 through 194 )
26X-RAY DIFFRACTION26chain 'A' and (resid 195 through 218 )
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 38 )
28X-RAY DIFFRACTION28chain 'D' and (resid 39 through 61 )
29X-RAY DIFFRACTION29chain 'D' and (resid 62 through 139 )
30X-RAY DIFFRACTION30chain 'D' and (resid 140 through 214 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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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