[English] 日本語
Yorodumi
- PDB-5i8e: Crystal Structure of Broadly Neutralizing HIV-1 Fusion Peptide-Ta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more