[English] 日本語
Yorodumi
- PDB-6ubi: N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ubi
TitleN123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
Components
  • HIV fusion peptide 512-519
  • VRC34.05 heavy chain
  • VRC34.05 light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV / neutralizing / antibody / fusion peptide / IMMUNE SYSTEM-VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / immunoglobulin complex / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / immunoglobulin complex / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / immune response / symbiont entry into host cell / 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
: / Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain ...: / Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Immunoglobulin gamma-1 heavy chain / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.903 Å
AuthorsXu, K. / Liu, K. / Kwong, P.D.
CitationJournal: Cell Host Microbe / Year: 2020
Title: VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage.
Authors: Shen, C.H. / DeKosky, B.J. / Guo, Y. / Xu, K. / Gu, Y. / Kilam, D. / Ko, S.H. / Kong, R. / Liu, K. / Louder, M.K. / Ou, L. / Zhang, B. / Chao, C.W. / Corcoran, M.M. / Feng, E. / Huang, J. / ...Authors: Shen, C.H. / DeKosky, B.J. / Guo, Y. / Xu, K. / Gu, Y. / Kilam, D. / Ko, S.H. / Kong, R. / Liu, K. / Louder, M.K. / Ou, L. / Zhang, B. / Chao, C.W. / Corcoran, M.M. / Feng, E. / Huang, J. / Normandin, E. / O'Dell, S. / Ransier, A. / Rawi, R. / Sastry, M. / Schmidt, S.D. / Wang, S. / Wang, Y. / Chuang, G.Y. / Doria-Rose, N.A. / Lin, B. / Zhou, T. / Boritz, E.A. / Connors, M. / Douek, D.C. / Karlsson Hedestam, G.B. / Sheng, Z. / Shapiro, L. / Mascola, J.R. / Kwong, P.D.
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VRC34.05 heavy chain
B: VRC34.05 light chain
C: HIV fusion peptide 512-519
D: VRC34.05 heavy chain
E: VRC34.05 light chain
F: HIV fusion peptide 512-519


Theoretical massNumber of molelcules
Total (without water)97,0066
Polymers97,0066
Non-polymers00
Water15,547863
1
A: VRC34.05 heavy chain
B: VRC34.05 light chain
C: HIV fusion peptide 512-519


Theoretical massNumber of molelcules
Total (without water)48,5033
Polymers48,5033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-33 kcal/mol
Surface area19160 Å2
MethodPISA
2
D: VRC34.05 heavy chain
E: VRC34.05 light chain
F: HIV fusion peptide 512-519


Theoretical massNumber of molelcules
Total (without water)48,5033
Polymers48,5033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-35 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.933, 44.278, 125.375
Angle α, β, γ (deg.)90.000, 96.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain E
13chain C
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 213
211chain DD1 - 214
112chain BB1 - 212
212chain EE1 - 212
113chain CC512 - 519
213chain FF512 - 519

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody VRC34.05 heavy chain


Mass: 24404.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Antibody VRC34.05 light chain


Mass: 23366.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6GMX0
#3: Protein/peptide HIV fusion peptide 512-519


Mass: 732.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7, 30% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 67167 / % possible obs: 96.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.077 / Rrim(I) all: 0.146 / Χ2: 1.609 / Net I/σ(I): 5.6 / Num. measured all: 229936
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.932.70.38127090.8150.2510.4580.95378.4
1.93-1.972.80.38928450.8130.2550.4670.98482.8
1.97-2.012.90.3530590.830.2280.4191.04388.1
2.01-2.0530.35531440.8440.2310.4251.10491.8
2.05-2.093.10.31632720.8880.2020.3771.15194.5
2.09-2.143.20.30433640.9010.1930.3611.23597
2.14-2.193.30.28334000.920.1780.3351.23698.3
2.19-2.253.40.2734260.9330.1680.3191.32199.4
2.25-2.323.50.2634710.9340.160.3051.32599.8
2.32-2.393.60.25234240.9340.1550.2971.378100
2.39-2.483.70.23134740.9490.140.2711.41399.9
2.48-2.583.70.21534740.9460.130.2511.53899.9
2.58-2.73.70.18634770.9610.1130.2181.58699.9
2.7-2.843.70.16134610.9710.0970.1881.70599.9
2.84-3.023.70.13734970.9740.0830.1611.828100
3.02-3.253.70.11634800.9820.0710.1361.95599.8
3.25-3.583.70.10134990.9820.0620.1192.30499.8
3.58-4.093.60.08535300.990.0520.0992.35399.7
4.09-5.163.60.07235150.990.0450.0852.42299.4
5.16-503.50.06636460.9910.0420.0792.07698.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→41.724 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2884 3402 5.07 %
Rwork0.2367 63719 -
obs0.2394 67121 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.96 Å2 / Biso mean: 24.4095 Å2 / Biso min: 7.47 Å2
Refinement stepCycle: final / Resolution: 1.903→41.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6664 0 0 863 7527
Biso mean---29.51 -
Num. residues----875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066824
X-RAY DIFFRACTIONf_angle_d1.1659257
X-RAY DIFFRACTIONf_chiral_restr0.0451042
X-RAY DIFFRACTIONf_plane_restr0.0061187
X-RAY DIFFRACTIONf_dihedral_angle_d13.9742437
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1902X-RAY DIFFRACTION9.114TORSIONAL
12D1902X-RAY DIFFRACTION9.114TORSIONAL
21B1927X-RAY DIFFRACTION9.114TORSIONAL
22E1927X-RAY DIFFRACTION9.114TORSIONAL
31C54X-RAY DIFFRACTION9.114TORSIONAL
32F54X-RAY DIFFRACTION9.114TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9032-1.93040.3333980.2948194270
1.9304-1.95920.33311090.2976219281
1.9592-1.98980.34741360.2922234585
1.9898-2.02240.32681300.2776244288
2.0224-2.05730.31911360.2885250392
2.0573-2.09470.32231530.2783259194
2.0947-2.1350.3321620.2827263296
2.135-2.17860.31671490.2697267898
2.1786-2.22590.30411420.2696273499
2.2259-2.27770.31281510.2658267799
2.2777-2.33470.26881390.24882809100
2.3347-2.39780.31221530.2582729100
2.3978-2.46830.35411310.25212796100
2.4683-2.5480.32271420.26682729100
2.548-2.6390.30611390.26222762100
2.639-2.74470.38851240.27722799100
2.7447-2.86960.31951540.26342741100
2.8696-3.02080.29851560.24842773100
3.0208-3.210.27631670.23412759100
3.21-3.45770.26861450.21632780100
3.4577-3.80550.29741390.21032807100
3.8055-4.35570.24391700.19522761100
4.3557-5.48570.22571320.1786284399
5.4857-41.720.23531450.212289599

+
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