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- PDB-7rdw: Crystal Structure of FH1 Fab bound to HXb2 HIV-1 gp120 core -

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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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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)

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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)

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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


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

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Non-polymers , 4 types, 102 molecules

#7: Chemical
ChemComp-NH4 / AMMONIUM ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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