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- PDB-5i8e: Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Ta... -

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Entry
Database: PDB / ID: 5i8e
TitleCrystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Targeting Antibody VRC34.01 Fab
Components
  • VRC34.01 Fab heavy chain
  • VRC34.01 Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / envelope / trimer / fusion peptide / antibody / neutralizing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.655 Å
AuthorsXu, K. / Zhou, T. / Liu, K. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2016
Title: Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody.
Authors: Rui Kong / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Thomas Lemmin / Kevin Liu / Gabriel Ozorowski / Cinque Soto / Justin D Taft / Robert T Bailer / Evan M Cale / Lei Chen / Chang W Choi ...Authors: Rui Kong / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Thomas Lemmin / Kevin Liu / Gabriel Ozorowski / Cinque Soto / Justin D Taft / Robert T Bailer / Evan M Cale / Lei Chen / Chang W Choi / Gwo-Yu Chuang / Nicole A Doria-Rose / Aliaksandr Druz / Ivelin S Georgiev / Jason Gorman / Jinghe Huang / M Gordon Joyce / Mark K Louder / Xiaochu Ma / Krisha McKee / Sijy O'Dell / Marie Pancera / Yongping Yang / Scott C Blanchard / Walther Mothes / Dennis R Burton / Wayne C Koff / Mark Connors / Andrew B Ward / Peter D Kwong / John R Mascola /
Abstract: The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the ...The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 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
A: VRC34.01 Fab heavy chain
B: VRC34.01 Fab light chain
C: VRC34.01 Fab heavy chain
D: VRC34.01 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,75214
Polymers93,0984
Non-polymers65410
Water2,252125
1
A: VRC34.01 Fab heavy chain
B: VRC34.01 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8767
Polymers46,5492
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-130 kcal/mol
Surface area19750 Å2
MethodPISA
2
C: VRC34.01 Fab heavy chain
D: VRC34.01 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8767
Polymers46,5492
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-130 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.606, 114.606, 174.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROchain AAA2 - 2132 - 222
21GLNGLNPROPROchain CCC1 - 2131 - 222
12ILEILEASNASNchain BBB2 - 2101 - 209
22ILEILEALAALAchain DDD2 - 2111 - 210

NCS ensembles :
ID
1
2

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Components

#1: Antibody VRC34.01 Fab heavy chain


Mass: 23668.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Homo sapiens (human)
#2: Antibody VRC34.01 Fab light chain


Mass: 22880.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Zinc Acetate, 0.1M Sodium Cacodylate pH6.5 and 15% PEG 8000

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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 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 30065 / % possible obs: 92.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 64.56 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.072 / Rrim(I) all: 0.144 / Χ2: 1.869 / Net I/av σ(I): 14.256 / Net I/σ(I): 12.9 / Num. measured all: 100033
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.65-2.743.30.807195.1
2.74-2.853.30.58194.4
2.85-2.983.40.379194.4
2.98-3.143.30.269194
3.14-3.343.40.193193.5
3.34-3.63.30.151193.2
3.6-3.963.30.133192.5
3.96-4.533.30.115192
4.53-5.713.30.11191.2
5.71-503.30.084188.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPI

4jpi


Resolution: 2.655→37.314 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 1535 5.11 %
Rwork0.1859 28530 -
obs0.1891 30065 92.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 251.28 Å2 / Biso mean: 82.4372 Å2 / Biso min: 32.35 Å2
Refinement stepCycle: final / Resolution: 2.655→37.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6411 0 10 125 6546
Biso mean--85.31 63.12 -
Num. residues----846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016572
X-RAY DIFFRACTIONf_angle_d1.5328937
X-RAY DIFFRACTIONf_chiral_restr0.061018
X-RAY DIFFRACTIONf_plane_restr0.0081138
X-RAY DIFFRACTIONf_dihedral_angle_d15.3832315
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1876X-RAY DIFFRACTION9.879TORSIONAL
12C1876X-RAY DIFFRACTION9.879TORSIONAL
21B1670X-RAY DIFFRACTION9.879TORSIONAL
22D1670X-RAY DIFFRACTION9.879TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6552-2.74080.42071480.30192644279294
2.7408-2.83880.34631330.25812629276295
2.8388-2.95240.26521570.21842603276094
2.9524-3.08670.28491570.20752604276194
3.0867-3.24930.31611340.20232614274894
3.2493-3.45280.27371380.17952602274093
3.4528-3.71910.22481440.17292603274793
3.7191-4.0930.25651440.16552569271392
4.093-4.68430.1941160.14722567268392
4.6843-5.89790.19581340.17262558269291
5.8979-37.31780.25251300.20312537266789
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)
11.0888-0.0507-0.25141.3122-0.24851.08970.098-0.1210.58040.05380.1380.3504-0.2312-0.27910.00080.53560.02610.13560.48540.08170.654739.40387.91331.52
21.40051.5385-1.41261.8058-1.65431.67940.5084-0.56070.69250.798-0.110.9046-0.48450.20320.30670.64360.29420.40430.83450.20041.165510.53786.12550.447
30.1369-0.08070.08520.04980.14010.30690.2516-0.39190.24020.80890.17780.67820.341-0.21780.31230.95840.26390.49620.99150.23240.963111.49485.53253.768
41.64420.37470.65471.2409-0.71771.03070.0376-0.36660.05510.19060.11670.12430.2023-0.01810.04450.6020.01160.13850.51750.05690.404636.79468.56942.356
51.61320.0459-0.06510.47880.27380.46720.12540.42640.25590.15330.30941.23630.2331-0.26750.07440.5332-0.19430.13390.99650.38641.17687.43369.82746.479
60.19690.214-0.18590.6106-0.22510.16850.2304-0.0569-0.7018-0.53740.0330.31640.0635-0.47970.02870.58010.0695-0.30060.67660.03230.828713.79855.0885.522
7-0.0039-0.14840.03572.0542-0.5360.12780.6167-0.0823-0.4348-0.2295-0.214-0.53630.3891-0.02190.07240.5661-0.102-0.28490.64690.10290.647920.96844.6944.871
80.41150.2185-0.32260.3181-0.28320.3294-0.42270.34840.99290.09791.0247-0.2077-0.2361-0.52150.06340.5231-0.0042-0.09210.46420.13350.648124.2960.2597.118
90.2969-0.2211-0.24380.2694-0.12370.69720.1405-0.49-0.22580.38520.1960.16460.1809-0.190.04190.5619-0.0901-0.16060.63980.13350.684622.96350.6514.549
100.28760.19360.02040.37190.07020.0170.06290.166-0.3123-0.02560.04940.3463-0.017-0.28310.00070.55380.0192-0.16030.73730.12340.693424.31255.7717.023
110.09940.00160.02280.3469-0.67571.2693-0.1881-0.3001-0.1386-0.5456-0.07770.33920.5749-0.113-0.22190.62460.1188-0.29360.77260.3180.82675.27975.521-7.861
120.89550.1504-0.85340.2714-0.6262.63920.13450.33170.7683-0.15080.10270.6612-1.18890.63010.49060.86190.0231-0.45050.8570.28660.84179.96277.751-13.68
130.5296-0.5878-0.40960.72380.62870.68190.3360.3266-0.56210.0724-0.00720.50520.20510.18-1.07290.9342-0.0291-0.43620.81760.36161.11010.38371.419-11.755
141.1640.01780.70641.0864-0.34341.0994-0.12770.42040.3536-0.2387-0.0030.106-0.1430.42860.09040.5989-0.0464-0.14570.58630.11550.43834.48167.326-2.168
150.48730.1393-0.56840.4727-0.13480.4722-0.10670.31551.10380.06890.1920.0247-0.1377-0.08290.00050.95360.0603-0.32860.67210.22761.187916.08689.871-6.809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:120 )A2 - 120
2X-RAY DIFFRACTION2( CHAIN A AND RESID 121:168 )A121 - 168
3X-RAY DIFFRACTION3( CHAIN A AND RESID 169:213 )A169 - 213
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:126 )B2 - 126
5X-RAY DIFFRACTION5( CHAIN B AND RESID 127:210 )B127 - 210
6X-RAY DIFFRACTION6( CHAIN C AND RESID 1:17 )C1 - 17
7X-RAY DIFFRACTION7( CHAIN C AND RESID 18:32 )C18 - 32
8X-RAY DIFFRACTION8( CHAIN C AND RESID 33:44 )C33 - 44
9X-RAY DIFFRACTION9( CHAIN C AND RESID 45:83 )C45 - 83
10X-RAY DIFFRACTION10( CHAIN C AND RESID 84:120 )C84 - 120
11X-RAY DIFFRACTION11( CHAIN C AND RESID 121:166 )C121 - 166
12X-RAY DIFFRACTION12( CHAIN C AND RESID 167:203 )C167 - 203
13X-RAY DIFFRACTION13( CHAIN C AND RESID 204:213 )C204 - 213
14X-RAY DIFFRACTION14( CHAIN D AND RESID 2:128 )D2 - 128
15X-RAY DIFFRACTION15( CHAIN D AND RESID 129:211 )D129 - 211

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