[English] 日本語
Yorodumi
- PDB-7n8q: Rhesusized RV305 DH677.3 Fab bound to Clade A/E 93TH057 HIV-1 gp1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n8q
TitleRhesusized RV305 DH677.3 Fab bound to Clade A/E 93TH057 HIV-1 gp120 core.
Components
  • (Rhesusized DH677.3 FAB ...) x 2
  • M48U1 CD4 MIMETIC PEPTIDE
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM / DH677.3 / HIV-1 Env V2 peptide / RV144 / RV305 / Rhesusized antibody
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: Front Immunol / Year: 2021
Title: Structure and Fc-Effector Function of Rhesusized Variants of Human Anti-HIV-1 IgG1s.
Authors: Tolbert, W.D. / Nguyen, D.N. / Tuyishime, M. / Crowley, A.R. / Chen, Y. / Jha, S. / Goodman, D. / Bekker, V. / Mudrak, S.V. / DeVico, A.L. / Lewis, G.K. / Theis, J.F. / Pinter, A. / Moody, M. ...Authors: Tolbert, W.D. / Nguyen, D.N. / Tuyishime, M. / Crowley, A.R. / Chen, Y. / Jha, S. / Goodman, D. / Bekker, V. / Mudrak, S.V. / DeVico, A.L. / Lewis, G.K. / Theis, J.F. / Pinter, A. / Moody, M.A. / Easterhoff, D. / Wiehe, K. / Pollara, J. / Saunders, K.O. / Tomaras, G.D. / Ackerman, M. / Ferrari, G. / Pazgier, M.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
N: M48U1 CD4 MIMETIC PEPTIDE
H: Rhesusized DH677.3 FAB HEAVY CHAIN
L: Rhesusized DH677.3 FAB LIGHT CHAIN
A: clade A/E 93TH057 HIV-1 gp120 core
C: Rhesusized DH677.3 FAB HEAVY CHAIN
D: Rhesusized DH677.3 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,33825
Polymers177,3577
Non-polymers3,98218
Water27015
1
G: clade A/E 93TH057 HIV-1 gp120 core
N: M48U1 CD4 MIMETIC PEPTIDE
H: Rhesusized DH677.3 FAB HEAVY CHAIN
L: Rhesusized DH677.3 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,19813
Polymers90,2074
Non-polymers1,9919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-0 kcal/mol
Surface area35870 Å2
MethodPISA
2
A: clade A/E 93TH057 HIV-1 gp120 core
C: Rhesusized DH677.3 FAB HEAVY CHAIN
D: Rhesusized DH677.3 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,14112
Polymers87,1503
Non-polymers1,9919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint3 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.182, 82.664, 111.899
Angle α, β, γ (deg.)90.00, 112.02, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 2 types, 4 molecules HCLD

#3: Antibody Rhesusized DH677.3 FAB HEAVY CHAIN


Mass: 24540.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Antibody Rhesusized DH677.3 FAB LIGHT CHAIN


Mass: 23252.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

-
Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 36 molecules GAN

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


Mass: 39356.613 Da / Num. of mol.: 2 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Protein/peptide M48U1 CD4 MIMETIC PEPTIDE


Mass: 3056.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 18
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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20% PEG 4000 0.1 M sodium citrate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 31091 / % possible obs: 82.7 % / Redundancy: 2.5 % / CC1/2: 0.975 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.078 / Net I/σ(I): 9.6
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1645 / CC1/2: 0.714 / Rpim(I) all: 0.467 / % possible all: 86

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.17.1refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFP

6mfp


Resolution: 2.9→47.93 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.877 / SU B: 74.4 / SU ML: 0.658 / Cross valid method: THROUGHOUT / ESU R Free: 0.594 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29578 1599 5.1 %RANDOM
Rwork0.25517 ---
obs0.2572 29478 82.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.955 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å2-1.3 Å2
2---0.66 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 2.9→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11790 0 252 15 12057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312345
X-RAY DIFFRACTIONr_bond_other_d0.0040.01711047
X-RAY DIFFRACTIONr_angle_refined_deg1.721.6816808
X-RAY DIFFRACTIONr_angle_other_deg1.5231.60125835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4851507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96224.048541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.357151987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.91539
X-RAY DIFFRACTIONr_chiral_restr0.0870.21709
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213563
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022385
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8164.0186096
X-RAY DIFFRACTIONr_mcbond_other3.8164.0186095
X-RAY DIFFRACTIONr_mcangle_it6.0836.0077576
X-RAY DIFFRACTIONr_mcangle_other6.0836.0077577
X-RAY DIFFRACTIONr_scbond_it4.0894.2626249
X-RAY DIFFRACTIONr_scbond_other4.0894.2626247
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2396.3119232
X-RAY DIFFRACTIONr_long_range_B_refined10.79275.61548382
X-RAY DIFFRACTIONr_long_range_B_other10.79275.61448377
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.973 Å
RfactorNum. reflection% reflection
Rfree0.394 142 -
Rwork0.378 2234 -
obs--85.47 %
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)
10.3877-0.19440.30960.1614-0.05830.8193-0.00630.03490.01940.04890.04540.0373-0.110.1399-0.03910.5122-0.0566-0.06180.3579-0.06770.2018-16.147511.73212.7075
20.10070.06270.1540.30490.23320.5842-0.0780.078-0.0887-0.00060.05870.0532-0.10040.13540.01930.54040.0237-0.0430.3738-0.05020.19616.109413.770859.2205
30.05150.0360.11290.35110.7161.52150.0354-0.1013-0.0053-0.0007-0.03850.01820.0151-0.10710.00310.5774-0.0114-0.12740.2702-0.03880.05091.55229.255568.5595
40.71690.25350.28550.12770.04660.7807-0.0838-0.0911-0.1187-0.030.0094-0.0517-0.0092-0.00350.07440.54330.0524-0.16150.3419-0.06360.1197-9.325-29.816325.2834
50.2259-0.1592-0.17850.3151-0.0030.49980.08640.01360.0456-0.0029-0.0310.0845-0.10340.1422-0.05540.5049-0.0288-0.09660.3837-0.03980.145823.1179-21.947569.8647
60.0877-0.07080.13380.46070.4941.27690.0586-0.02010.00330.02420.0634-0.00990.0667-0.0717-0.1220.4852-0.0509-0.08310.3544-0.01330.231210.8045-30.021880.2992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G1 - 492
2X-RAY DIFFRACTION2H1 - 215
3X-RAY DIFFRACTION3L1 - 214
4X-RAY DIFFRACTION4A1 - 492
5X-RAY DIFFRACTION5C1 - 215
6X-RAY DIFFRACTION6D1 - 214

+
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