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- PDB-5f6h: Crystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rh... -

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Basic information

Entry
Database: PDB / ID: 5f6h
TitleCrystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rhesus Macaque
Components
  • DH427 Antibody Heavy Chain
  • DH427 Antibody Light Chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV-1 / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsFera, D. / Harrison, S.C.
CitationJournal: Cell Rep / Year: 2016
Title: Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site.
Authors: Bradley, T. / Fera, D. / Bhiman, J. / Eslamizar, L. / Lu, X. / Anasti, K. / Zhang, R. / Sutherland, L.L. / Scearce, R.M. / Bowman, C.M. / Stolarchuk, C. / Lloyd, K.E. / Parks, R. / Eaton, A. ...Authors: Bradley, T. / Fera, D. / Bhiman, J. / Eslamizar, L. / Lu, X. / Anasti, K. / Zhang, R. / Sutherland, L.L. / Scearce, R.M. / Bowman, C.M. / Stolarchuk, C. / Lloyd, K.E. / Parks, R. / Eaton, A. / Foulger, A. / Nie, X. / Karim, S.S. / Barnett, S. / Kelsoe, G. / Kepler, T.B. / Alam, S.M. / Montefiori, D.C. / Moody, M.A. / Liao, H.X. / Morris, L. / Santra, S. / Harrison, S.C. / Haynes, B.F.
History
DepositionDec 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Sep 27, 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
Revision 1.5Oct 23, 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
L: DH427 Antibody Light Chain
K: DH427 Antibody Heavy Chain
J: DH427 Antibody Light Chain
N: DH427 Antibody Light Chain
P: DH427 Antibody Light Chain
I: DH427 Antibody Heavy Chain
M: DH427 Antibody Heavy Chain
O: DH427 Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)188,4178
Polymers188,4178
Non-polymers00
Water1,928107
1
L: DH427 Antibody Light Chain
K: DH427 Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,1042
Polymers47,1042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-25 kcal/mol
Surface area18800 Å2
MethodPISA
2
J: DH427 Antibody Light Chain
I: DH427 Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,1042
Polymers47,1042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-27 kcal/mol
Surface area18850 Å2
MethodPISA
3
N: DH427 Antibody Light Chain
M: DH427 Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,1042
Polymers47,1042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-27 kcal/mol
Surface area18960 Å2
MethodPISA
4
P: DH427 Antibody Light Chain
O: DH427 Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,1042
Polymers47,1042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-27 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.882, 153.786, 162.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain I
21chain K
31chain M
41chain O
12chain J
22chain L
32chain N
42chain P

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
11GLUGLUPROPROchain IIF1 - 2171 - 217
21GLUGLUPROPROchain KKB1 - 2171 - 217
31GLUGLUPROPROchain MMG1 - 2171 - 217
41GLUGLUPROPROchain OOH1 - 2171 - 217
12SERSERTHRTHRchain JJC2 - 2132 - 213
22SERSERTHRTHRchain LLA2 - 2132 - 213
32SERSERTHRTHRchain NND2 - 2132 - 213
42SERSERTHRTHRchain PPE2 - 2132 - 213

NCS ensembles :
ID
1
2

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Components

#1: Antibody
DH427 Antibody Light Chain


Mass: 22858.189 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#2: Antibody
DH427 Antibody Heavy Chain


Mass: 24246.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% PEG 2K MME, 100 mM sodium citrate, pH 4.0, 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2015
RadiationMonochromator: SINGLE CRYSTAL SI(220) SIDE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.66→48.9 Å / Num. obs: 55490 / % possible obs: 97.34 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 13.05
Reflection shellResolution: 2.69→2.74 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 1.3 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: separated Fv and Fc regions of I3.2 Fab from PDB Entry 4QHL

4qhl


Resolution: 2.66→48.897 Å / FOM work R set: 0.7842 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 2860 5.16 %
Rwork0.2303 52600 -
obs0.232 55460 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 27.05 Å2 / Biso min: 8.34 Å2
Refinement stepCycle: final / Resolution: 2.66→48.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12584 0 0 107 12691
Biso mean---15.82 -
Num. residues----1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412896
X-RAY DIFFRACTIONf_angle_d0.91217564
X-RAY DIFFRACTIONf_chiral_restr0.0332008
X-RAY DIFFRACTIONf_plane_restr0.0052236
X-RAY DIFFRACTIONf_dihedral_angle_d12.2144516
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11I3788X-RAY DIFFRACTION11.911TORSIONAL
12K3788X-RAY DIFFRACTION11.911TORSIONAL
13M3788X-RAY DIFFRACTION11.911TORSIONAL
14O3788X-RAY DIFFRACTION11.911TORSIONAL
21J3815X-RAY DIFFRACTION11.911TORSIONAL
22L3815X-RAY DIFFRACTION11.911TORSIONAL
23N3815X-RAY DIFFRACTION11.911TORSIONAL
24P3815X-RAY DIFFRACTION11.911TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6595-2.70540.3683980.33751623172161
2.7054-2.75460.36341270.32232502262994
2.7546-2.80750.37721580.315926412799100
2.8075-2.86490.40151370.296726872824100
2.8649-2.92710.31931420.306226612803100
2.9271-2.99520.34061450.304826812826100
2.9952-3.07010.35541530.317226372790100
3.0701-3.15310.3161430.289926622805100
3.1531-3.24590.32221410.271127052846100
3.2459-3.35060.28491420.257326612803100
3.3506-3.47030.26331400.245626832823100
3.4703-3.60920.30271470.237426802827100
3.6092-3.77340.27741520.229726862838100
3.7734-3.97230.25021670.208526462813100
3.9723-4.22110.20691660.192126842850100
4.2211-4.54680.19321430.17682719286299
4.5468-5.00390.19981370.17082701283899
5.0039-5.7270.21511570.18622708286599
5.727-7.21170.25231230.21312777290098
7.2117-48.90570.19421420.20212856299898
Refinement TLS params.Method: refined / Origin x: 1.7497 Å / Origin y: -1.0237 Å / Origin z: -29.7814 Å
111213212223313233
T0.0774 Å2-0.0315 Å20.0484 Å2-0.124 Å20.0193 Å2--0.1471 Å2
L-0.1136 °2-0.0438 °20.0907 °2-0.2417 °20.1986 °2--0.4556 °2
S-0.0142 Å °-0.0082 Å °-0.0395 Å °0.0388 Å °-0.0085 Å °0.0825 Å °0.045 Å °-0.0186 Å °0.0138 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allL2 - 213
2X-RAY DIFFRACTION1allK1 - 217
3X-RAY DIFFRACTION1allJ2 - 213
4X-RAY DIFFRACTION1allN2 - 213
5X-RAY DIFFRACTION1allP2 - 213
6X-RAY DIFFRACTION1allI1 - 217
7X-RAY DIFFRACTION1allM1 - 217
8X-RAY DIFFRACTION1allO1 - 217
9X-RAY DIFFRACTION1allA1 - 107

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