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- PDB-7yd3: Single-chain variable fragment of app 3D1 antibody -

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Basic information

Entry
Database: PDB / ID: 7yd3
TitleSingle-chain variable fragment of app 3D1 antibody
Components
  • heavy chain of 3D1 scFv
  • light chain of 3D1 scFv
KeywordsANTIMICROBIAL PROTEIN / Combinatorial antibody library / broad neutralizing mAb
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsYan, L. / Yang, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cross-reactive epitopes between HIV and Coronavirus revealed by 3D1
Authors: Yan, L. / Yang, G.
History
DepositionJul 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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

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Assembly

Deposited unit
H: heavy chain of 3D1 scFv
L: light chain of 3D1 scFv
A: heavy chain of 3D1 scFv
B: light chain of 3D1 scFv
C: heavy chain of 3D1 scFv
D: light chain of 3D1 scFv
E: heavy chain of 3D1 scFv
F: light chain of 3D1 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,96021
Polymers98,0048
Non-polymers95613
Water11,367631
1
H: heavy chain of 3D1 scFv
L: light chain of 3D1 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6694
Polymers24,5012
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-7 kcal/mol
Surface area10470 Å2
MethodPISA
2
A: heavy chain of 3D1 scFv
B: light chain of 3D1 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0689
Polymers24,5012
Non-polymers5677
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint6 kcal/mol
Surface area10000 Å2
MethodPISA
3
C: heavy chain of 3D1 scFv
D: light chain of 3D1 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5984
Polymers24,5012
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-13 kcal/mol
Surface area10250 Å2
MethodPISA
4
E: heavy chain of 3D1 scFv
F: light chain of 3D1 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6254
Polymers24,5012
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-10 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.183, 70.490, 74.815
Angle α, β, γ (deg.)108.830, 93.820, 90.090
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 120)
21chain C
31chain E
41chain H
12(chain B and resid 3 through 111)
22(chain D and resid 2 through 111)
32chain F
42(chain L and resid 1 through 110)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSER(chain A and resid 1 through 120)AC1 - 1201 - 120
21GLNGLNSERSERchain CCE1 - 1191 - 119
31GLNGLNSERSERchain EEG1 - 1191 - 119
41GLNGLNSERSERchain HHA1 - 1191 - 119
12ALAALAGLYGLY(chain B and resid 3 through 111)BD3 - 1113 - 111
22SERSERGLYGLY(chain D and resid 2 through 111)DF2 - 1112 - 111
32SERSERLEULEUchain FFH2 - 1102 - 110
42GLNGLNLEULEU(chain L and resid 1 through 110)LB1 - 1101 - 110

NCS ensembles :
ID
1
2

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Components

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Antibody , 2 types, 8 molecules HACELBDF

#1: Antibody
heavy chain of 3D1 scFv


Mass: 13041.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
light chain of 3D1 scFv


Mass: 11459.471 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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Non-polymers , 4 types, 644 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% 2-propanol, 0.1 M HEPES pH 7.5, 20% PEG 4000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.16→19.92 Å / Num. obs: 155752 / % possible obs: 94.4 % / Redundancy: 3.4 % / CC1/2: 0.91 / Net I/σ(I): 7.6
Reflection shellResolution: 2.16→2.24 Å / Num. unique obs: 45947 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KVF

6kvf


Resolution: 2.16→19.92 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.3 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 3826 4.36 %
Rwork0.2174 83984 -
obs0.219 87810 90.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.29 Å2 / Biso mean: 18.0401 Å2 / Biso min: 4.67 Å2
Refinement stepCycle: final / Resolution: 2.16→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6837 0 61 631 7529
Biso mean--20.16 23.02 -
Num. residues----915
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2190X-RAY DIFFRACTION10.521TORSIONAL
12C2190X-RAY DIFFRACTION10.521TORSIONAL
13E2190X-RAY DIFFRACTION10.521TORSIONAL
14H2190X-RAY DIFFRACTION10.521TORSIONAL
21B1932X-RAY DIFFRACTION10.521TORSIONAL
22D1932X-RAY DIFFRACTION10.521TORSIONAL
23F1932X-RAY DIFFRACTION10.521TORSIONAL
24L1932X-RAY DIFFRACTION10.521TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.190.4103600.28321389144941
2.19-2.220.32371310.2752573270475
2.22-2.250.36071330.28283021315486
2.25-2.280.3461410.26783019316087
2.28-2.310.32441290.25812936306587
2.31-2.350.27881760.24763297347393
2.35-2.390.28281310.24133132326394
2.39-2.430.26071550.24033266342194
2.43-2.470.3161530.24273230338394
2.47-2.520.31411340.24283238337294
2.52-2.570.28941400.23523235337593
2.57-2.630.3041680.23043221338993
2.63-2.690.27071620.22093124328692
2.69-2.760.28861220.22613241336392
2.76-2.830.27641290.22893041317089
2.83-2.910.23321340.21433287342195
2.91-3.010.22471420.21223236337894
3.01-3.110.23031630.21383287345095
3.11-3.240.21881380.22643249338794
3.24-3.380.25321300.21313299342994
3.38-3.560.26591570.21453191334894
3.56-3.780.25951600.21453138329892
3.78-4.070.21421440.18733316346096
4.07-4.480.19621500.16233313346395
4.48-5.120.18011540.16493243339795
5.12-6.410.22571370.19673248338594
6.41-19.920.24031530.24013214336793

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