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- PDB-6vpy: I33M (I3.2 mutant from CH103 Lineage) -

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Basic information

Entry
Database: PDB / ID: 6vpy
TitleI33M (I3.2 mutant from CH103 Lineage)
Components
  • I33M heavy chain
  • I33M light chain
KeywordsIMMUNE SYSTEM / FAB fragment / HIV-1 / antibody
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
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 ...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
IGH@ protein / IGL@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å
AuthorsFera, D. / Zhou, J.
Funding support United States, 5items
OrganizationGrant numberCountry
amfAR, The Foundation for AIDS Research109502-61-RKVA United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R15AI150484 - 01A1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/Office of Research Infrastructure Programs (NIH/ORIP)S10OD021527 United States
CitationJournal: Front Immunol / Year: 2020
Title: The Effects of Framework Mutations at the Variable Domain Interface on Antibody Affinity Maturation in an HIV-1 Broadly Neutralizing Antibody Lineage.
Authors: Zhou, J.O. / Zaidi, H.A. / Ton, T. / Fera, D.
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 9, 2020Group: Author supporting evidence / Data collection / Category: diffrn_detector / pdbx_audit_support / Item: _diffrn_detector.type
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: I33M light chain
A: I33M heavy chain
H: I33M heavy chain
L: I33M light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3937
Polymers95,1744
Non-polymers2203
Water5,459303
1
B: I33M light chain
A: I33M heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6223
Polymers47,5872
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-34 kcal/mol
Surface area19090 Å2
MethodPISA
2
H: I33M heavy chain
L: I33M light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7714
Polymers47,5872
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-27 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.605, 131.605, 104.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain H
12chain B
22chain L

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
11GLNGLNLYSLYSchain AAB1 - 2141 - 222
21GLNGLNLYSLYSchain HHC1 - 2141 - 222
12TYRTYRPROPROchain BBA2 - 2092 - 209
22SERSERPROPROchain LLD1 - 2091 - 209

NCS ensembles :
ID
1
2

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Components

#1: Antibody I33M light chain


Mass: 22692.061 Da / Num. of mol.: 2 / Fragment: FAB,FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293T / Plasmid: pVRC-8400 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8N355
#2: Antibody I33M heavy chain


Mass: 24894.764 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: Q6GMX6
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M ammonium sulfate, 100 mM HEPES, pH 7.23, 5% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97927 Å
DetectorType: DECTRIS EIGER X 16M / Detector: CCD / Date: Mar 2, 2018
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.352→50 Å / Num. obs: 42614 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 51.84 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.059 / Rrim(I) all: 0.139 / Χ2: 0.953 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.36-2.45.50.97421110.5040.4551.0790.69899.2
2.4-2.445.90.89221400.5420.4060.9830.70699.8
2.44-2.496.20.84121110.6530.3740.9220.756100
2.49-2.546.40.78821410.7130.3420.8610.747100
2.54-2.66.50.68421240.7430.2940.7460.809100
2.6-2.666.30.5721010.820.2480.6230.906100
2.66-2.726.20.49521420.8350.2170.5411.018100
2.72-2.86.10.43921450.8630.1950.4811.057100
2.8-2.885.80.36421110.890.1670.4011.10999.9
2.88-2.975.20.27921330.9450.1360.3121.10499.7
2.97-3.085.90.24921520.9450.1140.2751.081100
3.08-3.26.40.21221240.9720.0930.2321.097100
3.2-3.356.20.18221330.9690.0810.21.06399.9
3.35-3.535.90.14821280.9760.0690.1641.06399.8
3.53-3.755.60.12221550.9840.0580.1351.02499.4
3.75-4.035.30.10621000.9850.0520.1190.98898.6
4.03-4.444.40.08120780.9890.0440.0931.03396.4
4.44-5.085.30.06621320.9930.0330.0740.97699
5.08-6.460.05821430.9960.0260.0640.91599.5
6.4-505.80.04122100.9980.0180.0450.97299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.29 Å113.92 Å
Translation5.29 Å113.92 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.7.17phasing
Cootmodel building
PHENIX1.8.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4QHL

4qhl


Resolution: 2.36→47.65 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.83
RfactorNum. reflection% reflection
Rfree0.2232 2014 4.73 %
Rwork0.1854 --
obs0.1872 42571 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.82 Å2 / Biso mean: 53.22 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.36→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 13 303 6662
Biso mean--22.26 55.92 -
Num. residues----851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076555
X-RAY DIFFRACTIONf_angle_d1.1428955
X-RAY DIFFRACTIONf_chiral_restr0.0481033
X-RAY DIFFRACTIONf_plane_restr0.0061145
X-RAY DIFFRACTIONf_dihedral_angle_d13.2162285
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1894X-RAY DIFFRACTION11.087TORSIONAL
12H1894X-RAY DIFFRACTION11.087TORSIONAL
21B1851X-RAY DIFFRACTION11.087TORSIONAL
22L1851X-RAY DIFFRACTION11.087TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.36-2.41060.27281310.2552272894
2.4106-2.47580.30051430.24912923100
2.4758-2.54860.27751100.2392931100
2.5486-2.63090.27681590.22472903100
2.6309-2.72490.24931400.21582896100
2.7249-2.8340.2411380.21082912100
2.834-2.96290.24381610.20452900100
2.9629-3.11910.23521440.19952918100
3.1191-3.31450.24861580.18262902100
3.3145-3.57030.2271610.17632896100
3.5703-3.92950.19971420.1661290999
3.9295-4.49770.18341390.153283597
4.4977-5.66520.211310.1628292599
5.6652-47.650.22211570.20262979100
Refinement TLS params.Method: refined / Origin x: 65.733 Å / Origin y: 8.7101 Å / Origin z: 28.7986 Å
111213212223313233
T0.4024 Å20.0005 Å20.0131 Å2-0.328 Å20.0173 Å2--0.3686 Å2
L0.2776 °20.0466 °20.374 °2-0.06 °20.0687 °2--0.3146 °2
S-0.1031 Å °-0.0036 Å °0.0496 Å °-0.0103 Å °0.0217 Å °0.0399 Å °-0.1036 Å °-0.0039 Å °0.1003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB2 - 209
2X-RAY DIFFRACTION1allA1 - 214
3X-RAY DIFFRACTION1allH1 - 214
4X-RAY DIFFRACTION1allL1 - 209
5X-RAY DIFFRACTION1allS1 - 317
6X-RAY DIFFRACTION1allS318 - 330
7X-RAY DIFFRACTION1allC1
8X-RAY DIFFRACTION1allG2 - 3

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