[English] 日本語
Yorodumi
- PDB-4lst: Crystal structure of broadly and potently neutralizing antibody V... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lst
TitleCrystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade C strain ZM176.66 gp120
Components
  • ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
  • HEAVY CHAIN OF ANTIBODY VRC01
  • LIGHT CHAIN OF ANTIBODY VRC01
Keywordsviral protein/immune system / Neutralizing antibody VRC01 / HIV envelope glycoprotein gp120 / antibody antigen / viral protein-immune system 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
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsZhou, T. / Moquin, S. / Kwong, P.D.
CitationJournal: Immunity / Year: 2013
Title: Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies.
Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / ...Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / McKee, K. / Schramm, C.A. / Skinner, J. / Yang, Y. / Yang, Z. / Zhang, Z. / Zheng, A. / Bonsignori, M. / Haynes, B.F. / Scheid, J.F. / Nussenzweig, M.C. / Simek, M. / Burton, D.R. / Koff, W.C. / Mullikin, J.C. / Connors, M. / Shapiro, L. / Nabel, G.J. / Mascola, J.R. / Kwong, P.D.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3May 7, 2014Group: Other
Revision 1.4Jul 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
H: HEAVY CHAIN OF ANTIBODY VRC01
L: LIGHT CHAIN OF ANTIBODY VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,61111
Polymers86,8423
Non-polymers1,7708
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint7 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.105, 77.981, 200.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C


Mass: 39273.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: ZM176.66 / Gene: env / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: R4GRV3
#2: Antibody HEAVY CHAIN OF ANTIBODY VRC01


Mass: 24395.684 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): HEK 293F / Production host: Homo sapiens (human)
#3: Antibody LIGHT CHAIN OF ANTIBODY VRC01


Mass: 23172.686 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): HEK 293F / Production host: Homo sapiens (human)
#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.: 8
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 0.1M Tris, 11.8% PEG 4000, 0.2M Na-Acetate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: APS 22-BM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 32759 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.086 / Net I/σ(I): 10.5
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.321 / % possible all: 56

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_998refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→40.68 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 1.36 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1649 5.05 %
Rwork0.19 --
obs0.193 32670 91.9 %
all-35565 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.91 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 104.99 Å2
Baniso -1Baniso -2Baniso -3
1-7.8265 Å20 Å2-0 Å2
2--10.6871 Å2-0 Å2
3----18.5135 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 112 71 6171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046258
X-RAY DIFFRACTIONf_angle_d0.8968487
X-RAY DIFFRACTIONf_dihedral_angle_d13.0632305
X-RAY DIFFRACTIONf_chiral_restr0.06954
X-RAY DIFFRACTIONf_plane_restr0.0041083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5522-2.62730.3377920.28411618X-RAY DIFFRACTION58
2.6273-2.71210.31531010.28341982X-RAY DIFFRACTION71
2.7121-2.8090.34541340.28332385X-RAY DIFFRACTION87
2.809-2.92140.37231380.27722678X-RAY DIFFRACTION96
2.9214-3.05440.3321390.2622750X-RAY DIFFRACTION99
3.0544-3.21530.32471390.2422805X-RAY DIFFRACTION99
3.2153-3.41670.26241530.22532768X-RAY DIFFRACTION99
3.4167-3.68030.28431260.20882780X-RAY DIFFRACTION100
3.6803-4.05040.27671460.18652799X-RAY DIFFRACTION99
4.0504-4.63580.2181440.14782800X-RAY DIFFRACTION99
4.6358-5.83790.20641630.15732802X-RAY DIFFRACTION98
5.8379-40.6860.19241740.17862854X-RAY DIFFRACTION95
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)
13.769-1.82190.82417.3658-2.11474.35970.10350.18930.2463-0.0405-0.212-0.55560.46820.61640.15970.6193-0.07190.07540.8397-0.07180.539834.00786.23096.4288
23.56490.7037-0.40433.7512-1.73966.3759-0.0750.6827-0.1497-0.45210.11420.4140.6567-0.207-0.02850.7244-0.1054-0.01620.6584-0.10240.512311.50293.84925.1994
37.5069-2.0111-0.316.29770.96627.5836-0.0235-0.34220.64160.3291-0.0417-0.0069-0.2435-0.26170.08480.5341-0.0615-0.05350.5177-0.02990.40996.250919.571527.22
49.23592.18241.21297.7928-3.01184.85440.1821-0.329-0.06160.41550.08550.4346-0.1669-0.1626-0.25141.15330.08860.02880.7194-0.06310.6714-21.518419.942659.5296
57.195-1.6998-2.72744.4976-0.54248.0259-0.2817-0.8379-0.10020.81120.1112-0.12930.70490.06710.14680.86090.017-0.0710.6977-0.03110.460513.02529.038846.3702
66.61620.27262.04392.07071.24485.84220.39260.149-0.981-0.05340.36780.30320.9185-0.1082-0.7241.3145-0.0262-0.22810.55970.0080.9336-15.3275.199961.253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G and (resid 44:253 or resid 476:492)
2X-RAY DIFFRACTION2chain G and resid 254:475
3X-RAY DIFFRACTION3chain H and resid 1:114
4X-RAY DIFFRACTION4chain H and resid 115:216
5X-RAY DIFFRACTION5chain L and resid 1:108
6X-RAY DIFFRACTION6chain L and resid 109:216

+
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://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