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- PDB-4s1s: Crystal structure of a VRC01-lineage antibody, 45-VRC01.H5.F-1859... -

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Basic information

Entry
Database: PDB / ID: 4s1s
TitleCrystal structure of a VRC01-lineage antibody, 45-VRC01.H5.F-185917, in complex with clade A/E HIV-1 gp120 core
Components
  • Fab of VRC01 light chain
  • Fab of VRC01-lineage antibody,45-VRC01.H5.F-185917 heavy chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM/INHIBITOR / HIV-1 / neutralizing antibodies / VRC01-lineage / antibody maturation / evolutionary rate / VIRAL PROTEIN-IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / 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
clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 Å
AuthorsKwon, Y.D. / Yang, Y. / Zhang, B. / Kwong, P.D.
CitationJournal: Cell(Cambridge,Mass.) / 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 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 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

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
H: Fab of VRC01-lineage antibody,45-VRC01.H5.F-185917 heavy chain
L: Fab of VRC01 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,54114
Polymers87,0913
Non-polymers2,45011
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint23 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.386, 67.662, 266.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39211.434 Da / Num. of mol.: 1 / Fragment: residue 44-492 / Mutation: V1V2 and V3 deletion
Source method: isolated from a genetically manipulated source
Details: HIV-1 gp120 core / Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: clade A/E 93TH057 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9*PLUS
#2: Antibody Fab of VRC01-lineage antibody,45-VRC01.H5.F-185917 heavy chain


Mass: 24790.045 Da / Num. of mol.: 1
Fragment: Fab of VRC01-lineage antibody,45-VRC01.H5.F-185917 heavy chain
Source method: isolated from a genetically manipulated source
Details: codon-optimized VRC01-lineage antibody, 45-VRC01.H5.F-185917, heavy chain
Source: (gene. exp.) Homo sapiens (human) / Gene: Heavy chain / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody Fab of VRC01 light chain


Mass: 23089.572 Da / Num. of mol.: 1 / Fragment: Fab of VRC01 light chain / Mutation: N72T
Source method: isolated from a genetically manipulated source
Details: codon-optimized human antibody VRC01 light chain / Source: (gene. exp.) Homo sapiens (human) / Gene: Light chain / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#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.: 10
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
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

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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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8000, 5% iso-propanol, 0.1M HEPES, 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.39→50 Å / Num. all: 14657 / Num. obs: 14247 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 92.5 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.097 / Net I/σ(I): 14.4
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 1.63 / Rsym value: 0.499 / % possible all: 82.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE8

3se8


Resolution: 3.39→47.496 Å / SU ML: 0.49 / σ(F): 1.34 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2996 698 4.92 %
Rwork0.2619 --
obs0.2636 14188 96.77 %
all-14661 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.39→47.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 155 0 6187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036356
X-RAY DIFFRACTIONf_angle_d0.9048665
X-RAY DIFFRACTIONf_dihedral_angle_d11.3052333
X-RAY DIFFRACTIONf_chiral_restr0.037979
X-RAY DIFFRACTIONf_plane_restr0.0051107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3887-3.65030.33691310.34492358X-RAY DIFFRACTION87
3.6503-4.01750.35291350.32012653X-RAY DIFFRACTION97
4.0175-4.59840.29961360.27212767X-RAY DIFFRACTION100
4.5984-5.79190.28971450.24182781X-RAY DIFFRACTION100
5.7919-47.50080.27591510.22682931X-RAY DIFFRACTION100
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)
13.1634-0.95971.35694.98710.81116.95410.14020.2043-1.0968-1.8290.04710.9241.61640.2247-0.28351.2201-0.1564-0.43030.5976-0.05510.9292-36.1245-83.0654-57.6306
23.15390.69522.97154.53520.50533.10280.72440.0806-0.124-0.96260.21752.92441.4168-0.35770.08560.8322-0.3743-0.65060.6032-0.00871.4101-40.7874-80.3087-54.91
33.22230.27280.83593.75010.03773.4213-0.07540.06580.7884-0.60250.3583.7835-1.3551-0.7101-0.1030.09710.1212-0.3310.94520.06272.2165-43.3448-60.12-52.6198
43.7623-0.3625-0.67032.3362-0.54053.8893-0.00250.15610.0367-1.56950.38351.8210.0498-0.110.42060.8597-0.0844-0.39540.79160.40451.1672-35.3299-57.7442-61.1437
52.1878-0.65861.15394.6642-0.49644.70740.0977-0.10450.074-0.66940.43972.49330.2144-0.0323-0.11250.2699-0.1329-0.08020.7423-0.0941.0975-38.6822-67.5775-51.0271
65.71681.56331.24337.89891.8446.0178-0.37190.43640.44021.2033-0.2809-0.3103-0.61670.390.50280.717-0.0588-0.21260.5507-0.01660.4974-18.3738-55.6148-40.6701
78.27351.3677-5.33872.59791.49636.16970.5677-0.08640.76140.2912-0.0220.057-1.69570.53483.94071.3453-0.1749-0.60220.46970.04420.9007-18.7891-45.2809-39.1625
86.5178-0.71610.93557.32993.14897.0349-0.0460.2053-1.57261.914-0.7507-0.1333-0.04660.57110.15391.0256-0.1664-0.18790.541-0.15890.2979-19.6266-65.579-38.1702
91.08321.28850.97364.24224.4324.2498-0.1071-0.08310.9771-0.556-1.3024-0.08-0.59261.1283-0.69331.1539-0.326-0.46350.6617-0.04230.8496-12.9988-49.2684-32.198
109.879-1.27410.88626.99475.27495.6829-0.4051-2.00770.34921.00161.96781.09-1.6499-0.0085-1.04571.9280.184-0.27071.1580.17460.9995-5.1115-27.6229-1.1477
116.7007-0.428-0.74485.85142.27512.9546-0.17970.87121.55270.07561.23-0.0204-0.99610.8575-0.7581.3521-0.332-0.47771.16570.23541.0592-3.0142-35.0411-15.3255
127.82990.14090.3734.705-0.06967.25990.4172-0.37911.61750.27461.5197-1.5081-1.54851.4559-0.57771.7724-0.4382-0.40431.1017-0.21631.16212.7353-28.2752-9.3059
130.6104-0.17270.86612.96410.60594.52340.0777-0.80280.05113.247-0.5444-0.5442-0.2262-0.66470.27512.9052-0.44360.01370.9671-0.29310.5669-20.7827-61.1291-11.5759
143.00640.6769-1.64745.98060.20957.0547-0.0956-0.51-0.82592.6469-1.0764-0.52390.8087-0.3774-0.81222.3122-0.0822-0.05220.5696-0.05140.2338-18.2646-67.5083-22.7743
152.3797-2.21861.77064.00290.4778.2706-0.172-0.6807-0.12952.7658-0.67320.24050.5721-1.1319-0.01722.5827-0.49150.03010.75320.02340.5415-21.0984-64.9702-18.0419
168.7081.0716-0.7292.11121.40512.6637-0.0153-0.54591.8517-1.4548-0.10780.46811.40610.0583-0.4322.05040.0615-0.32590.9354-0.02950.6367-10.1887-37.2334-5.62
174.86961.8274-2.45723.9695-0.1961.80570.3583-0.43220.4470.65920.28160.72820.8504-1.5401-0.12271.7784-0.1381-0.47671.49820.14840.6604-14.9248-39.6848-2.8697
186.76040.1448-3.39714.54961.85612.51830.31830.16451.0962-0.1677-0.54410.75931.3912-1.0561-0.13371.6964-0.078-0.48431.4219-0.28431.0373-12.8879-41.2168-6.2389
196.50940.4937-3.28267.49911.55282.86260.3488-1.33591.82840.2251-0.05781.087-0.5969-2.0293-0.62631.5294-0.0368-0.14821.4779-0.10421.3094-19.146-31.1268-3.2619
203.0695-1.9386-0.54148.616-1.70241.67150.1297-0.25843.01110.7059-0.2970.1441-0.5448-0.3796-0.72861.72030.28550.13131.2903-0.26541.7911-15.6597-23.93391.9591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND RESID 44:200 )G44 - 200
2X-RAY DIFFRACTION2( CHAIN G AND RESID 201:258 )G201 - 258
3X-RAY DIFFRACTION3( CHAIN G AND RESID 259:395 )G259 - 395
4X-RAY DIFFRACTION4( CHAIN G AND RESID 396:434 )G396 - 434
5X-RAY DIFFRACTION5( CHAIN G AND RESID 435:492 )G435 - 492
6X-RAY DIFFRACTION6( CHAIN H AND RESID 1:76 )H1 - 76
7X-RAY DIFFRACTION7( CHAIN H AND RESID 77:90 )H77 - 90
8X-RAY DIFFRACTION8( CHAIN H AND RESID 91:107 )H91 - 107
9X-RAY DIFFRACTION9( CHAIN H AND RESID 108:130 )H108 - 130
10X-RAY DIFFRACTION10( CHAIN H AND RESID 131:146 )H131 - 146
11X-RAY DIFFRACTION11( CHAIN H AND RESID 147:188 )H147 - 188
12X-RAY DIFFRACTION12( CHAIN H AND RESID 189:216 )H189 - 216
13X-RAY DIFFRACTION13( CHAIN L AND RESID 3:24 )L3 - 24
14X-RAY DIFFRACTION14( CHAIN L AND RESID 25:59 )L25 - 59
15X-RAY DIFFRACTION15( CHAIN L AND RESID 60:96 )L60 - 96
16X-RAY DIFFRACTION16( CHAIN L AND RESID 97:126 )L97 - 126
17X-RAY DIFFRACTION17( CHAIN L AND RESID 127:146 )L127 - 146
18X-RAY DIFFRACTION18( CHAIN L AND RESID 147:170 )L147 - 170
19X-RAY DIFFRACTION19( CHAIN L AND RESID 171:200 )L171 - 200
20X-RAY DIFFRACTION20( CHAIN L AND RESID 201:210 )L201 - 210

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