[English] 日本語
Yorodumi
- PDB-7rdw: Crystal Structure of FH1 Fab bound to HXb2 HIV-1 gp120 core -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rdw
TitleCrystal Structure of FH1 Fab bound to HXb2 HIV-1 gp120 core
Components
  • (FH1 Fab Heavy ...) x 2
  • FH1 Fab Light Chain
  • Glycoprotein 120
KeywordsIMMUNE SYSTEM / FH1 / VH1-2*02 / VRC01 / Antibody / HIV-1
Function / homologyAMMONIUM ION
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsWeidle, C. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2022
Title: Characterization of a vaccine-elicited human antibody with sequence homology to VRC01-class antibodies that binds the C1C2 gp120 domain.
Authors: Gray, M.D. / Feng, J. / Weidle, C.E. / Cohen, K.W. / Ballweber-Fleming, L. / MacCamy, A.J. / Huynh, C.N. / Trichka, J.J. / Montefiori, D. / Ferrari, G. / Pancera, M. / McElrath, M.J. / Stamatatos, L.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Glycoprotein 120
D: Glycoprotein 120
G: FH1 Fab Heavy Chain
H: FH1 Fab Heavy Chain
I: FH1 Fab Light Chain
L: FH1 Fab Light Chain
M: Glycoprotein 120
N: Glycoprotein 120
Q: FH1 Fab Heavy Chain
R: FH1 Fab Light Chain
U: FH1 Fab Heavy Chain
V: FH1 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,28557
Polymers356,01312
Non-polymers9,27345
Water1,60389
1
C: Glycoprotein 120
Q: FH1 Fab Heavy Chain
R: FH1 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,40316
Polymers89,0123
Non-polymers2,39113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-16 kcal/mol
Surface area34370 Å2
MethodPISA
2
D: Glycoprotein 120
U: FH1 Fab Heavy Chain
V: FH1 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,86312
Polymers88,9953
Non-polymers1,8699
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-23 kcal/mol
Surface area34610 Å2
MethodPISA
3
G: FH1 Fab Heavy Chain
I: FH1 Fab Light Chain
N: Glycoprotein 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,87316
Polymers88,9953
Non-polymers2,87913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint2 kcal/mol
Surface area36300 Å2
MethodPISA
4
H: FH1 Fab Heavy Chain
L: FH1 Fab Light Chain
M: Glycoprotein 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,14613
Polymers89,0123
Non-polymers2,13410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-12 kcal/mol
Surface area34470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.361, 106.266, 113.219
Angle α, β, γ (deg.)67.566, 76.674, 60.987
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 4 molecules CDMN

#1: Protein
Glycoprotein 120


Mass: 41336.422 Da / Num. of mol.: 4 / Fragment: HXB2 gp120 core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): 293 / Production host: Homo sapiens (human)

-
Antibody , 3 types, 8 molecules GUHQILRV

#2: Antibody FH1 Fab Heavy Chain


Mass: 24472.371 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: Antibody FH1 Fab Heavy Chain


Mass: 24489.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 / Production host: Homo sapiens (human)
#4: Antibody
FH1 Fab Light Chain


Mass: 23185.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 2 types, 32 molecules

#5: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 28
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

-
Non-polymers , 4 types, 102 molecules

#7: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NH4SO4, 20% PEG 1500, 0.1M Tris pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50.18 Å / Num. obs: 36171 / % possible obs: 92.5 % / Redundancy: 1.6 % / Biso Wilson estimate: 62.36 Å2 / CC1/2: 0.95 / Net I/σ(I): 5.29
Reflection shellResolution: 3.5→3.56 Å / Num. unique obs: 1577 / CC1/2: 0.712 / % possible all: 69.3

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-20001.15.2_3472data reduction
SCALEPACKdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFT

6mft


Resolution: 3.55→50.18 Å / SU ML: 0.4539 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.1724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2949 1840 5.09 %
Rwork0.2602 34318 -
obs0.2619 36158 76.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.99 Å2
Refinement stepCycle: LAST / Resolution: 3.55→50.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21828 0 43 90 21961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007822378
X-RAY DIFFRACTIONf_angle_d1.621930673
X-RAY DIFFRACTIONf_chiral_restr0.07763584
X-RAY DIFFRACTIONf_plane_restr0.00293986
X-RAY DIFFRACTIONf_dihedral_angle_d14.84927618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.640.3227250.3006503X-RAY DIFFRACTION14.75
3.64-3.750.3617820.30921263X-RAY DIFFRACTION37.25
3.75-3.870.3298970.28731753X-RAY DIFFRACTION51.2
3.87-4.010.34371150.27872185X-RAY DIFFRACTION63.55
4.01-4.170.3111150.27142585X-RAY DIFFRACTION74.57
4.17-4.360.30161390.25822906X-RAY DIFFRACTION83.33
4.36-4.590.31621580.25033140X-RAY DIFFRACTION91.48
4.59-4.880.26251790.23193343X-RAY DIFFRACTION96.57
4.88-5.250.28412080.23023262X-RAY DIFFRACTION96.85
5.25-5.780.28241770.25543346X-RAY DIFFRACTION97.13
5.78-6.610.30221760.28723403X-RAY DIFFRACTION98
6.61-8.330.30611910.28213323X-RAY DIFFRACTION97.37
8.33-50.180.26351780.25133306X-RAY DIFFRACTION96.03

+
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