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- PDB-4qhk: UCA (unbound) from CH103 Lineage -

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Basic information

Entry
Database: PDB / ID: 4qhk
TitleUCA (unbound) from CH103 Lineage
Components
  • UCA heavy chain
  • UCA 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.487 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 / 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
M: UCA heavy chain
I: UCA heavy chain
O: UCA heavy chain
K: UCA heavy chain
N: UCA light chain
J: UCA light chain
L: UCA light chain
P: UCA light chain


Theoretical massNumber of molelcules
Total (without water)190,6888
Polymers190,6888
Non-polymers00
Water0
1
M: UCA heavy chain
N: UCA light chain


Theoretical massNumber of molelcules
Total (without water)47,6722
Polymers47,6722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-23 kcal/mol
Surface area19560 Å2
MethodPISA
2
I: UCA heavy chain
J: UCA light chain


Theoretical massNumber of molelcules
Total (without water)47,6722
Polymers47,6722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-23 kcal/mol
Surface area19280 Å2
MethodPISA
3
O: UCA heavy chain
P: UCA light chain


Theoretical massNumber of molelcules
Total (without water)47,6722
Polymers47,6722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-20 kcal/mol
Surface area19590 Å2
MethodPISA
4
K: UCA heavy chain
L: UCA light chain


Theoretical massNumber of molelcules
Total (without water)47,6722
Polymers47,6722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-22 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.691, 71.148, 184.402
Angle α, β, γ (deg.)90.000, 93.810, 90.000
Int Tables number4
Space group name H-MP1211
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
11VALVALSERSERchain IIB2 - 2152 - 223
21VALVALSERSERchain KKD2 - 2152 - 223
31VALVALLYSLYSchain MMA2 - 2142 - 222
41VALVALLYSLYSchain OOC2 - 2142 - 222
12TYRTYRTHRTHRchain JJF2 - 2092 - 210
22TYRTYRTHRTHRchain LLG2 - 2092 - 210
32TYRTYRTHRTHRchain NNE2 - 2092 - 210
42TYRTYRTHRTHRchain PPH2 - 2092 - 210

NCS ensembles :
ID
1
2

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Components

#1: Antibody
UCA heavy chain


Mass: 24887.803 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
UCA light chain


Mass: 22784.156 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)

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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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2013
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: 3.487→50 Å / Num. obs: 25281 / % possible obs: 96.5 % / Redundancy: 3 % / Biso Wilson estimate: 43.03 Å2 / Rmerge(I) obs: 0.144 / Χ2: 0.907 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.487-3.5630.37312690.905195.1
3.56-3.632.90.34612330.982197
3.63-3.692.90.30412601.022197.8
3.69-3.7730.26512430.885194.4
3.77-3.852.90.27812570.927199.1
3.85-3.9430.24212670.904195
3.94-4.042.90.1912530.856199.3
4.04-4.1530.18812560.909195.6
4.15-4.2730.16212830.877199.3
4.27-4.4130.14812740.89195.7
4.41-4.5730.14212390.832198.1
4.57-4.753.10.12112850.968197.2
4.75-4.9730.12312420.904196
4.97-5.2330.11812760.871196.9
5.23-5.5530.11512670.844197.2
5.55-5.982.90.11312711.009195.9
5.98-6.5830.10212590.911195.6
6.58-7.533.10.08612680.942197.2
7.53-9.483.10.06312820.896195.5
9.48-503.10.05412970.826193.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.49 Å46.85 Å
Translation3.49 Å46.85 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 23851
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
12.99-10059.30.322508
10.28-12.99620.669506
8.97-10.2858.20.676509
8.1-8.9760.60.703536
7.45-8.1640.688601
6.93-7.4566.50.695635
6.51-6.9369.30.656677
6.15-6.5168.10.666714
5.85-6.1565.70.672753
5.59-5.8567.20.659791
5.36-5.5964.20.702845
5.16-5.3660.60.722861
4.97-5.1659.20.686908
4.81-4.9760.30.71878
4.66-4.8158.70.723977
4.53-4.6658.70.707982
4.4-4.5359.90.678971
4.29-4.4580.6881006
4.18-4.2962.40.6851008
4.08-4.1864.60.6621064
3.99-4.0866.10.6671076
3.9-3.9972.40.6491064
3.82-3.969.90.6161089
3.75-3.82690.631044
3.68-3.7566.30.5851044
3.61-3.68730.5431043
3.49-3.6172.40.5231761

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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: 3.487→46.846 Å / FOM work R set: 0.7345 / SU ML: 0.28 / σ(F): 1.98 / Phase error: 32.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2849 1207 5.08 %
Rwork0.2687 --
obs0.2696 23782 90.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.68 Å2 / Biso mean: 66.91 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.487→46.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12800 0 0 0 12800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513280
X-RAY DIFFRACTIONf_angle_d1.18318140
X-RAY DIFFRACTIONf_chiral_restr0.0432078
X-RAY DIFFRACTIONf_plane_restr0.0062294
X-RAY DIFFRACTIONf_dihedral_angle_d13.1744684
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11I3868X-RAY DIFFRACTION13.93TORSIONAL
12K3868X-RAY DIFFRACTION13.93TORSIONAL
13M3868X-RAY DIFFRACTION13.93TORSIONAL
14O3868X-RAY DIFFRACTION13.93TORSIONAL
21J3688X-RAY DIFFRACTION13.93TORSIONAL
22L3688X-RAY DIFFRACTION13.93TORSIONAL
23N3688X-RAY DIFFRACTION13.93TORSIONAL
24P3688X-RAY DIFFRACTION13.93TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.487-3.62690.3182910.32121937202870
3.6269-3.79190.34411320.31152316244884
3.7919-3.99180.37371100.30192463257390
3.9918-4.24170.26211410.28092584272593
4.2417-4.5690.2981430.24862564270793
4.569-5.02830.25951400.23592676281696
5.0283-5.75470.2591560.24892665282196
5.7547-7.2460.29821410.2742692283396
7.246-46.85050.23471530.24472678283193
Refinement TLS params.Method: refined / Origin x: 2.8125 Å / Origin y: -24.2999 Å / Origin z: 53.5362 Å
111213212223313233
T0.3935 Å20.0013 Å20.0218 Å2-0.4799 Å20.0024 Å2--0.444 Å2
L-0.0138 °20.0061 °20.0371 °2-0.0043 °2-0.056 °2--0.1355 °2
S0.0169 Å °-0.0759 Å °0.0012 Å °0.1375 Å °-0.0074 Å °0.0089 Å °-0.0025 Å °-0.0181 Å °-0.0071 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allM2 - 214
2X-RAY DIFFRACTION1allI2 - 215
3X-RAY DIFFRACTION1allO2 - 214
4X-RAY DIFFRACTION1allK2 - 215
5X-RAY DIFFRACTION1allN2 - 209
6X-RAY DIFFRACTION1allJ2 - 209
7X-RAY DIFFRACTION1allL2 - 209
8X-RAY DIFFRACTION1allP2 - 209

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