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- PDB-4qhm: I3.1 (unbound) from CH103 Lineage -

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Basic information

Entry
Database: PDB / ID: 4qhm
TitleI3.1 (unbound) from CH103 Lineage
Components
  • I2 light chain
  • I3 heavy chain
KeywordsIMMUNE SYSTEM / Fab fragment / HIV-1 / antibody
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.23 Å
AuthorsFera, D. / Harrison, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains.
Authors: Fera, D. / Schmidt, A.G. / Haynes, B.F. / Gao, F. / Liao, H.X. / Kepler, T.B. / Harrison, S.C.
History
DepositionMay 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: I3 heavy chain
E: I3 heavy chain
C: I3 heavy chain
G: I3 heavy chain
F: I2 light chain
B: I2 light chain
D: I2 light chain
H: I2 light chain


Theoretical massNumber of molelcules
Total (without water)191,0088
Polymers191,0088
Non-polymers00
Water00
1
A: I3 heavy chain
B: I2 light chain


Theoretical massNumber of molelcules
Total (without water)47,7522
Polymers47,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-26 kcal/mol
Surface area19320 Å2
MethodPISA
2
E: I3 heavy chain
F: I2 light chain


Theoretical massNumber of molelcules
Total (without water)47,7522
Polymers47,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area19250 Å2
MethodPISA
3
C: I3 heavy chain
D: I2 light chain


Theoretical massNumber of molelcules
Total (without water)47,7522
Polymers47,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-26 kcal/mol
Surface area19120 Å2
MethodPISA
4
G: I3 heavy chain
H: I2 light chain


Theoretical massNumber of molelcules
Total (without water)47,7522
Polymers47,7522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-27 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.311, 132.311, 209.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Antibody
I3 heavy chain


Mass: 24894.764 Da / Num. of mol.: 4 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293T / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6*PLUS
#2: Antibody
I2 light chain


Mass: 22857.270 Da / Num. of mol.: 4 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293T / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM sodium acetate, pH 5.0, 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. all: 33948 / Num. obs: 33930 / % possible obs: 98.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 77.74 Å2 / Rmerge(I) obs: 0.114 / Χ2: 0.873 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.23-3.2920.6531230.586197.6
3.29-3.3520.56332610.616198
3.35-3.4120.46332540.619198
3.41-3.4820.39632490.71197.9
3.48-3.5520.3731510.712198.3
3.55-3.6420.30332480.725198.4
3.64-3.7320.25432290.883198.5
3.73-3.8320.24432690.748198.9
3.83-3.941.90.21732910.897199
3.94-4.071.90.15332820.87199.3
4.07-4.211.90.12932280.94199.3
4.21-4.381.90.10733030.968199.4
4.38-4.581.90.09633130.961199.6
4.58-4.821.90.08632401.061199.7
4.82-5.131.90.07832621.048199.6
5.13-5.521.90.07833161.094199.5
5.52-6.081.90.08332580.944199.5
6.08-6.951.90.06632680.967199.2
6.95-8.751.90.04332321.142198
8.75-5020.039331711100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.81 Å48.04 Å
Translation4.81 Å48.04 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 37606
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
13.42-10058.60.095502
10.51-13.4248.90.74539
8.93-10.5142.30.832640
7.89-8.9351.90.807733
7.15-7.8957.70.757819
6.59-7.1561.70.746877
6.14-6.5960.90.757955
5.77-6.1460.90.7371016
5.46-5.7759.10.7621085
5.2-5.4658.60.7581131
4.97-5.257.10.7871180
4.77-4.9759.70.7771222
4.59-4.77640.7451276
4.43-4.5958.30.7621333
4.28-4.4359.70.7551391
4.15-4.2858.10.7251415
4.03-4.1564.20.7141457
3.92-4.0366.10.6941505
3.82-3.92680.6631536
3.73-3.8268.50.6551596
3.64-3.7367.80.6591627
3.56-3.6467.80.6341640
3.48-3.5668.50.6631661
3.41-3.4870.70.6261732
3.34-3.4174.10.621768
3.28-3.3472.50.6191820
3.22-3.2874.60.6121802
3.12-3.2277.10.5673348

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
DM6.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JAN

4jan


Resolution: 3.23→48.036 Å / FOM work R set: 0.8098 / SU ML: 0.36 / σ(F): 1.37 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1709 5.04 %
Rwork0.2244 --
obs0.2258 33905 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.54 Å2 / Biso mean: 85.5 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.23→48.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12840 0 0 0 12840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413184
X-RAY DIFFRACTIONf_angle_d0.97818004
X-RAY DIFFRACTIONf_chiral_restr0.0662068
X-RAY DIFFRACTIONf_plane_restr0.0042292
X-RAY DIFFRACTIONf_dihedral_angle_d13.9434632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.23-3.3250.33141340.305826542788
3.325-3.43230.32371330.280426742807
3.4323-3.5550.33751400.28726382778
3.555-3.69730.28451410.272127032844
3.6973-3.86550.31011430.272526312774
3.8655-4.06920.34851200.246327202840
4.0692-4.32390.24161650.212726372802
4.3239-4.65750.24021490.189326612810
4.6575-5.12580.19951490.181626872836
5.1258-5.86640.21851360.194926982834
5.8664-7.38670.27481450.224527362881
7.3867-48.04120.18261540.199827572911
Refinement TLS params.Method: refined / Origin x: 65.8985 Å / Origin y: -8.6675 Å / Origin z: -13.5854 Å
111213212223313233
T0.4298 Å20.0156 Å2-0.0293 Å2-0.3549 Å20.0142 Å2--0.3669 Å2
L0.6345 °20.1709 °2-0.3319 °2-0.1682 °2-0.0125 °2--0.2641 °2
S-0.0223 Å °0.0422 Å °-0.0024 Å °0.0387 Å °-0.0004 Å °-0.0005 Å °-0.0229 Å °-0.0242 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 215
2X-RAY DIFFRACTION1allE1 - 215
3X-RAY DIFFRACTION1allC1 - 215
4X-RAY DIFFRACTION1allG1 - 215
5X-RAY DIFFRACTION1allF2 - 209
6X-RAY DIFFRACTION1allB2 - 209
7X-RAY DIFFRACTION1allD2 - 209
8X-RAY DIFFRACTION1allH2 - 209

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